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Mixed fixes. #264

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merged 4 commits into from May 15, 2015
Merged

Mixed fixes. #264

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22d4a1d
dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.
nsoranzo May 15, 2015
224d8f3
Remove numpy requirement, not used since commit 09ce7a9b1793b0400f7e6…
nsoranzo May 15, 2015
341a6cf
Use requirements of type="package" instead of deprecated "binary".
nsoranzo May 15, 2015
48023ed
Remove outdated sentence.
nsoranzo May 15, 2015
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3 changes: 0 additions & 3 deletions config/plugins/visualizations/README.txt
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Expand Up @@ -8,9 +8,6 @@ Properly configured and written visualizations will be accessible to
the user when they click the 'visualizations' icon for a dataset
in their history panel.

The framework must be enabled in your 'galaxy.ini' file by uncommenting (and
having a valid path for) the 'visualizations_plugin_directory' entry.

For more information, see http://wiki.galaxyproject.org/VisualizationsRegistry


Expand Down
26 changes: 13 additions & 13 deletions tools/data_source/bed_convert.xml
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@@ -1,14 +1,14 @@
<tool id="BED File Converter1" name="BED File Converter" version="1.0.0">
<description>creates a bed or xbed file containing from text query</description>
<command>noop</command>
<inputs>
<display>creates a bed or xbed file containing user assigned input of $input</display>
<param format="tabular" name="input" type="data" />
<param name="chrom" size="4" type="text" value="all" />
</inputs>
<outputs>
<data format="bed" name="out_file1" />
</outputs>
<help>User specifies delimiter, header information, and column assignments and the file will be converted to BED or xBED.
</help>
<tool id="BED File Converter1" name="BED File Converter" version="1.0.0">
<description>creates a bed or xbed file containing from text query</description>
<command>noop</command>
<inputs>
<display>creates a bed or xbed file containing user assigned input of $input</display>
<param format="tabular" name="input" type="data" />
<param name="chrom" size="4" type="text" value="all" />
</inputs>
<outputs>
<data format="bed" name="out_file1" />
</outputs>
<help>User specifies delimiter, header information, and column assignments and the file will be converted to BED or xBED.
</help>
</tool>
50 changes: 25 additions & 25 deletions tools/data_source/genbank.xml
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@@ -1,25 +1,25 @@
<tool id="genbank" name="Connect to Genbank" version="1.0.0">
<!-- <description>queries genbank</description> -->
<command interpreter="python">genbank.py $mode "$text" $output</command>
<inputs>
<param name="mode" type="select">
<option value="nucleotide">nucleotide database</option>
<option value="protein">proteins database</option>
<label>Get sequences from the</label>
</param>
<param name="text" size="40" type="text" value="6273291">
<label>with accession ID</label>
</param>
</inputs>
<outputs>
<data format="fasta" name="output" />
</outputs>
<help>
At the moment this tool allows the following simple searches:
- by GI: **51594135**
- by accession: **CF622840**
- using text: **human hbb1** (this feature is experimental)
</help>
</tool>
<tool id="genbank" name="Connect to Genbank" version="1.0.0">
<!-- <description>queries genbank</description> -->
<command interpreter="python">genbank.py $mode "$text" $output</command>
<inputs>
<param name="mode" type="select">
<option value="nucleotide">nucleotide database</option>
<option value="protein">proteins database</option>
<label>Get sequences from the</label>
</param>
<param name="text" size="40" type="text" value="6273291">
<label>with accession ID</label>
</param>
</inputs>
<outputs>
<data format="fasta" name="output" />
</outputs>
<help>
At the moment this tool allows the following simple searches:

- by GI: **51594135**
- by accession: **CF622840**
- using text: **human hbb1** (this feature is experimental)
</help>

</tool>
54 changes: 27 additions & 27 deletions tools/data_source/import.xml
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@@ -1,27 +1,27 @@
<tool id="Featured datasets4" name="Featured datasets" version="1.0.0">
<description>(PSU prepared queries)</description>
<command interpreter="python">import.py $data $output</command>
<inputs>
<display>$data</display>
<param name="data" type="select" display="radio">
<option value="eryth">Erythroid predicted cis-regulatory modules</option>
<option value="exons">Exons of protein-coding genes in the mouse genome, assembly mm3</option>
<option value="cishg16 ">Known cis-regulatory modules in the human HBB gene complex (hg16)</option>
<option value="cishg17">Known cis-regulatory modules in the human HBB gene complex (hg17)</option>
<option value="krhg16">Known regulatory regions (hg16)</option>
<option value="krhg17">Known regulatory regions (hg17)</option>
<option value="tARhg16mmc">Human (hg16) evolutionary cold region (vs mouse)</option>
<option value="tARhg16mmm">Human (hg16) evolutionary medium region (vs mouse)</option>
<option value="tARhg16mmh">Human (hg16) evolutionary hot region (vs mouse)</option>
<option value="tARhg16rnc">Human (hg16) evolutionary cold region (vs rat)</option>
<option value="tARhg16rnm">Human (hg16) evolutionary medium region (vs rat)</option>
<option value="tARhg16rnh">Human (hg16) evolutionary hot region (vs rat)</option>
<option value="phastConsHg16">phastCons hg16 (stringent, top ~5%) from UCSC</option>
<option value="omimhg16">OMIM disorders (hg16)</option>
<option value="omimhg17">OMIM disorders (hg17)</option>
</param>
</inputs>
<outputs>
<data format="bed" name="output" />
</outputs>
</tool>
<tool id="Featured datasets4" name="Featured datasets" version="1.0.0">
<description>(PSU prepared queries)</description>
<command interpreter="python">import.py $data $output</command>
<inputs>
<display>$data</display>
<param name="data" type="select" display="radio">
<option value="eryth">Erythroid predicted cis-regulatory modules</option>
<option value="exons">Exons of protein-coding genes in the mouse genome, assembly mm3</option>
<option value="cishg16 ">Known cis-regulatory modules in the human HBB gene complex (hg16)</option>
<option value="cishg17">Known cis-regulatory modules in the human HBB gene complex (hg17)</option>
<option value="krhg16">Known regulatory regions (hg16)</option>
<option value="krhg17">Known regulatory regions (hg17)</option>
<option value="tARhg16mmc">Human (hg16) evolutionary cold region (vs mouse)</option>
<option value="tARhg16mmm">Human (hg16) evolutionary medium region (vs mouse)</option>
<option value="tARhg16mmh">Human (hg16) evolutionary hot region (vs mouse)</option>
<option value="tARhg16rnc">Human (hg16) evolutionary cold region (vs rat)</option>
<option value="tARhg16rnm">Human (hg16) evolutionary medium region (vs rat)</option>
<option value="tARhg16rnh">Human (hg16) evolutionary hot region (vs rat)</option>
<option value="phastConsHg16">phastCons hg16 (stringent, top ~5%) from UCSC</option>
<option value="omimhg16">OMIM disorders (hg16)</option>
<option value="omimhg17">OMIM disorders (hg17)</option>
</param>
</inputs>
<outputs>
<data format="bed" name="output" />
</outputs>
</tool>
228 changes: 114 additions & 114 deletions tools/data_source/microbial_import.xml
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@@ -1,114 +1,114 @@
<tool id="microbial_import1" name="Get Microbial Data" version="1.0.0">
<command interpreter="python">microbial_import.py $CDS,$tRNA,$rRNA,$sequence,$GeneMark,$GeneMarkHMM,$Glimmer3 $output ${GALAXY_DATA_INDEX_DIR}/microbial_data.loc</command>
<inputs>
<param name="kingdom" type="select" label="Select the Desired Kingdom">
<options from_file="microbial_data.loc" startswith="ORG">
<column name="name" index="3"/>
<column name="value" index="3"/>
<filter type="unique_value" name="unique" column="3"/>
</options>
</param>
<param name="org" type="select" label="Select the Desired Organism">
<options from_file="microbial_data.loc" startswith="ORG">
<column name="name" index="2"/>
<column name="value" index="1"/>
<filter type="param_value" ref="kingdom" name="kingdom" column="3"/>
<filter type="sort_by" column="2"/>
</options>
</param>
<param name="CDS" type="select" label="Select Desired Coding Sequences" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="CDS" column="4"/>
</options>
</param>
<param name="tRNA" type="select" label="Select Desired tRNA" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="tRNA" column="4"/>
</options>
</param>
<param name="rRNA" type="select" label="Select Desired rRNA" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="rRNA" column="4"/>
</options>
</param>
<param name="sequence" type="select" label="Select Desired DNA Sequences" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="sequence" column="4"/>
</options>
</param>
<param name="GeneMark" type="select" label="Select Desired GeneMark Annotations" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="GeneMark" column="4"/>
</options>
</param>
<param name="GeneMarkHMM" type="select" label="Select Desired GeneMarkHMM Annotations" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="GeneMarkHMM" column="4"/>
</options>
</param>
<param name="Glimmer3" type="select" label="Select Desired Glimmer3 Annotations" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="Glimmer3" column="4"/>
</options>
</param>
</inputs>
<outputs>
<data format="bed" name="output"/>
</outputs>
<code file="microbial_import_code.py"/>
<help>
This tool will allow you to obtain various genomic datasets for any completed Microbial Genome Project as listed at NCBI_.
.. _NCBI: http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1
Current datasets available include
1. CDS
2. tRNA
3. rRNA
4. FASTA Sequences
5. GeneMark Annotations
6. GeneMarkHMM Annotations
7. Glimmer3 Annotations
-----
Organisms in **bold** are available at the UCSC Browser.
-----
.. class:: infomark
**Note:** Having trouble locating your organism? Click here_ for a list of available species and their location.
.. _here: https://wiki.galaxyproject.org/Main/Data%20Libraries/Microbes
</help>
</tool>
<tool id="microbial_import1" name="Get Microbial Data" version="1.0.0">
<command interpreter="python">microbial_import.py $CDS,$tRNA,$rRNA,$sequence,$GeneMark,$GeneMarkHMM,$Glimmer3 $output ${GALAXY_DATA_INDEX_DIR}/microbial_data.loc</command>
<inputs>
<param name="kingdom" type="select" label="Select the Desired Kingdom">
<options from_file="microbial_data.loc" startswith="ORG">
<column name="name" index="3"/>
<column name="value" index="3"/>
<filter type="unique_value" name="unique" column="3"/>
</options>
</param>
<param name="org" type="select" label="Select the Desired Organism">
<options from_file="microbial_data.loc" startswith="ORG">
<column name="name" index="2"/>
<column name="value" index="1"/>
<filter type="param_value" ref="kingdom" name="kingdom" column="3"/>
<filter type="sort_by" column="2"/>
</options>
</param>
<param name="CDS" type="select" label="Select Desired Coding Sequences" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="CDS" column="4"/>
</options>
</param>
<param name="tRNA" type="select" label="Select Desired tRNA" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="tRNA" column="4"/>
</options>
</param>
<param name="rRNA" type="select" label="Select Desired rRNA" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="rRNA" column="4"/>
</options>
</param>
<param name="sequence" type="select" label="Select Desired DNA Sequences" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="sequence" column="4"/>
</options>
</param>
<param name="GeneMark" type="select" label="Select Desired GeneMark Annotations" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="GeneMark" column="4"/>
</options>
</param>
<param name="GeneMarkHMM" type="select" label="Select Desired GeneMarkHMM Annotations" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="GeneMarkHMM" column="4"/>
</options>
</param>
<param name="Glimmer3" type="select" label="Select Desired Glimmer3 Annotations" display="checkboxes" multiple="True">
<options from_file="microbial_data.loc" startswith="DATA">
<column name="name" index="3"/>
<column name="value" index="1"/>
<column name="feature" index="4"/>
<filter type="param_value" ref="org" name="kingdom" column="2"/>
<filter type="static_value" name="feature" value="Glimmer3" column="4"/>
</options>
</param>
</inputs>
<outputs>
<data format="bed" name="output"/>
</outputs>
<code file="microbial_import_code.py"/>
<help>

This tool will allow you to obtain various genomic datasets for any completed Microbial Genome Project as listed at NCBI_.

.. _NCBI: http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?view=1

Current datasets available include
1. CDS
2. tRNA
3. rRNA
4. FASTA Sequences
5. GeneMark Annotations
6. GeneMarkHMM Annotations
7. Glimmer3 Annotations

-----

Organisms in **bold** are available at the UCSC Browser.

-----

.. class:: infomark

**Note:** Having trouble locating your organism? Click here_ for a list of available species and their location.

.. _here: https://wiki.galaxyproject.org/Main/Data%20Libraries/Microbes
</help>
</tool>