amm made minor edits to citation titles in xmls

McIntyre-Lab · Jan 15, 2021 · fc4c1b6 · fc4c1b6
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diff --git a/galaxy/BWASplitSAM_2output.xml b/galaxy/BWASplitSAM_2output.xml
@@ -65,7 +65,7 @@ Example summary output file::
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/NBmodel_stan2_galaxy.xml b/galaxy/NBmodel_stan2_galaxy.xml
@@ -190,7 +190,7 @@ Headers:
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/calculate_priors_from_ase_count_tables.xml b/galaxy/calculate_priors_from_ase_count_tables.xml
@@ -131,7 +131,7 @@ Header descriptions::
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/check_aln_design_file.xml b/galaxy/check_aln_design_file.xml
@@ -79,7 +79,7 @@ Example design file for simulated data ::
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/check_comparate_design_file.xml b/galaxy/check_comparate_design_file.xml
@@ -11,7 +11,7 @@
     --out=$out
 ]]></command>
     <inputs>
-        <param name="design" type="data" format="tabular,tsv" label="Select Comparate Design File" help="Design file containing comparates and conditions. Please refer to the BASE User Guide for help."/>
+        <param name="design" type="data" format="tabular,tsv" label="Select Comparate Design File" help="Design file containing comparates and conditions. Please refer to the BayesASE User Guide for help."/>
         <param name="compNum" size="30" type="select" value="" display="radio" label="Comparate Number" help="Select the number of comparate conditions for the data.">
             <option value="1">One Comparate</option>
             <option value="2">Two Comparates</option>
@@ -56,7 +56,7 @@ An example design file for two comparates::
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }

diff --git a/galaxy/check_for_lost_reads.xml b/galaxy/check_for_lost_reads.xml
@@ -83,7 +83,7 @@ The BayesASE align and count workflow should be rerun if flag_start_readNum_eq_r
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/check_sam_present.xml b/galaxy/check_sam_present.xml
@@ -75,7 +75,7 @@ Example of output:
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/check_samcomp_for_lost_reads.xml b/galaxy/check_samcomp_for_lost_reads.xml
@@ -106,7 +106,7 @@ An example of an unsuccessful output file where reads were lost:
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/combine_cnt_tables.xml b/galaxy/combine_cnt_tables.xml
@@ -156,7 +156,7 @@ Example Sample Design File:
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/create_sam_file_with_features.xml b/galaxy/create_sam_file_with_features.xml
@@ -27,7 +27,7 @@
     <help><![CDATA[
     **Tool Description**
 
-This tool reformats the SAM file containing uniquely mapping reads using the multi-column BED file created by the *Remove reads that do not overlap with a feature for BASE* tool.
+This tool reformats the SAM file containing uniquely mapping reads using the multi-column BED file created by the *Remove reads that do not overlap with a feature for BayesASE* tool.
 The resulting SAM file contains the name of genic features in the 'chrom' field.
 
 
@@ -61,7 +61,7 @@ Example input BED file
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/drop_reads_that_doNot_overlap_after_BEDtools_intersect.xml b/galaxy/drop_reads_that_doNot_overlap_after_BEDtools_intersect.xml
@@ -69,7 +69,7 @@ Example output BED file:
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/gen_headers_after_merge_priors_one_comparate.xml b/galaxy/gen_headers_after_merge_priors_one_comparate.xml
@@ -107,7 +107,7 @@ Example of output::
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/merge_comparates_and_gen_headers_for_bayesian.xml b/galaxy/merge_comparates_and_gen_headers_for_bayesian.xml
@@ -101,7 +101,7 @@ Example of Output::
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/merge_priors_to_comparate.xml b/galaxy/merge_priors_to_comparate.xml
@@ -113,7 +113,7 @@ Example output for comparate W55_M::
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/reformat_bedfile.xml b/galaxy/reformat_bedfile.xml
@@ -64,7 +64,7 @@ A 4-column BED file that has the names of the Feature IDs in the first column an
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/reformat_sample_design_file.xml b/galaxy/reformat_sample_design_file.xml
@@ -87,7 +87,7 @@ Example of Priors Design File::
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison Morse, Elyse Borgert, Gavin Gamble, Fei Zhou, Jeremy Newman, Fabio Marroni, Lauren M. McIntyre},
-            title = {BASE: Bayesian analysis of allele specific expression reveals statistically significant regulatory variation},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/sam2bed.xml b/galaxy/sam2bed.xml
@@ -57,7 +57,7 @@ The tool outputs a 3-column BED file containing the following fields for each un
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/sam_compare_w_feature.xml b/galaxy/sam_compare_w_feature.xml
@@ -144,7 +144,7 @@ Example of ASE Totals Table::
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>

diff --git a/galaxy/summarize_sam_compare_cnts_table_1cond.xml b/galaxy/summarize_sam_compare_cnts_table_1cond.xml
@@ -34,8 +34,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="design" value="BASE_testdata/summarize_counts_testdata/summarization_df_BASE.tabular" ftype="tabular"/>
-            <param name="collection" value="BASE_testdata/summarize_counts_testdata/combined_ASE_counts_tables_BASE" ftype="data_collection"/>
+            <param name="design" value="summarize_counts_testdata/summarization_df_BASE.tabular" ftype="tabular"/>
+            <param name="collection" value="summarize_counts_testdata/combined_ASE_counts_tables_BASE" ftype="data_collection"/>
             <param name="parent1" value="G1" ftype="text"/>
             <param name="parent2" value="G2" ftype="text"/>
             <param name="sampleIDcol" value="sampleID" ftype="text"/>
@@ -146,7 +146,7 @@ Column header definitions::
     <citations>
             <citation type="bibtex">@ARTICLE{Miller20BASE,
             author = {Brecca Miller, Alison M. Morse, Elyse Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy Newman, Luis Leon Novello, Fabio Marroni, Lauren M. McIntyre},
-            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BASE)},
+            title = {Testcrosses are an efficient strategy for identifying cis regulatory variation: Bayesian analysis of allele imbalance among conditions (BayesASE)},
             journal = {G3},
             year = {2021}
             }</citation>