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Update main, adding deeptools and gemini.
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Dave Bouvier authored and g2main committed Mar 21, 2016
1 parent 3f3a833 commit 3c83d6d
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42 changes: 42 additions & 0 deletions files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml
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<label id="454" text="Roche-454 data" version="" />
<label id="solid" text="AB-SOLiD data" version="" />
</section>
<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.2.2.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.2.2.0" />
</section>
<section id="ngs_mapping" name="NGS: Mapping" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1" />
Expand Down Expand Up @@ -858,4 +875,29 @@
<tool id="echo_main_w2_handler2" />
<tool id="echo_main_stampede" />
<tool id="echo_main_cluster" />
<section id="ngs:_gemini" name="NGS: Gemini" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_pathways/gemini_pathways/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_roh/gemini_roh/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_fusions/gemini_fusions/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_dump/gemini_dump/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_gene_wise/gemini_gene_wise/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_comp_hets/gemini_comp_hets/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_mendel_errors/gemini_mendel_errors/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_region/gemini_region/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_recessive_and_dominant/gemini_recessive_and_dominant/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_qc/gemini_qc/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_interactions/gemini_interactions/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_amend/gemini_amend/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_lof_sieve/gemini_lof_sieve/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_burden/gemini_burden/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_windower/gemini_windower/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_actionable_mutations/gemini_actionable_mutations/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_stats/gemini_stats/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_set_somatic/gemini_set_somatic/0.18.1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_de_novo/gemini_de_novo/0.18.1.0" />
</section>
</toolbox>
72 changes: 72 additions & 0 deletions files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml
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Expand Up @@ -35,5 +35,77 @@
</output>
</data_table>
</data_manager>
<data_manager guid="toolshed.g2.bx.psu.edu/repos/bgruening/data_manager_diamond_database_builder/data_manager/diamond_database_builder/0.0.1" id="diamond_database_builder" shed_conf_file="/srv/galaxy/main/var/shed_tool_conf.xml" version="0.0.1">
<tool file="toolshed.g2.bx.psu.edu/repos/bgruening/data_manager_diamond_database_builder/ce62d0912b10/data_manager_diamond_database_builder/data_manager/data_manager_diamond_database_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/data_manager_diamond_database_builder/diamond_database_builder/0.0.1"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_diamond_database_builder</repository_name><repository_owner>bgruening</repository_owner><installed_changeset_revision>ce62d0912b10</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/bgruening/data_manager_diamond_database_builder/diamond_database_builder/0.0.1</id><version>0.0.1</version></tool><data_table name="diamond_database">
<output>
<column name="value" />
<column name="name" />
<column name="db_path" output_ref="out_file">
<move relativize_symlinks="True" type="directory">
<!-- <source>${db_path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">diamond_database/${value}</target>
</move>
<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/diamond_database/${value}/${db_path}</value_translation>
<value_translation type="function">abspath</value_translation>
</column>
</output>
</data_table>
</data_manager>



<data_manager guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/data_manager/twobit_builder/0.0.1" id="twobit_builder" shed_conf_file="/srv/galaxy/main/var/shed_tool_conf.xml" version="0.0.1">
<tool file="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/74b09c8e5f6e/data_manager_twobit_builder/data_manager/twobit_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/twobit_builder_data_manager/0.0.1"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_twobit_builder</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>74b09c8e5f6e</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/twobit_builder_data_manager/0.0.1</id><version>0.0.1</version></tool><data_table name="lastz_seqs">
<output>
<column name="value" />
<column name="name" />
<column name="path" output_ref="out_file">
<move type="file">
<source>${path}</source>
<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/seq/${path}</target>
</move>
<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/seq/${path}</value_translation>
</column>
</output>
</data_table>

<data_table name="twobit">
<output>
<column name="value" />
<column name="path" output_ref="out_file"><!-- move happens above -->
<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/seq/${path}</value_translation>
</column>
</output>
</data_table>

<data_table name="alignseq_seq">
<output>
<column name="type" /><!-- always seq -->
<column name="value" /><!-- also dbkey -->
<column name="path" output_ref="out_file"><!-- move happens above -->
<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/seq/${path}</value_translation>
</column>
</output>
</data_table>

</data_manager>



<data_manager guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager/data_manager_gemini_download/0.0.1" id="data_manager_gemini_download" shed_conf_file="/srv/galaxy/main/var/shed_tool_conf.xml">
<tool file="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/345412d58d75/data_manager_gemini_database_downloader/data_manager/data_manager_gemini_download.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager_gemini_download/0.18.1"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_gemini_database_downloader</repository_name><repository_owner>iuc</repository_owner><installed_changeset_revision>345412d58d75</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager_gemini_download/0.18.1</id><version>0.18.1</version></tool><data_table name="gemini_databases"> <!-- Defines a Data Table to be modified. -->
<output> <!-- Handle the output of the Data Manager Tool -->
<column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
<column name="dbkey" /> <!-- columns that are going to be specified by the Data Manager Tool -->
<column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool -->
<column name="path" output_ref="out_file">
<move relativize_symlinks="True" type="directory">
<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">gemini/data/${dbkey}/${value}</target>
</move>
<value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/gemini/data/${dbkey}/${value}/gemini/data/</value_translation>
<value_translation type="function">abspath</value_translation>
</column>
</output>
</data_table>
</data_manager>
</data_managers>

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