Question: Sub groups within galaxy shed tool conf file
0
gravatar for djevo1
14 months ago by
djevo160
djevo160 wrote:

How do you add subsections to the shed tool conf file so tools can be grouped under each drop-down according to package. Example would be cufflinks and deseq are both under differential expression, but I would like a sub heading above each tool group that says cufflinks and deseq.

rna-seq toolshed galaxy • 406 views
ADD COMMENTlink modified 14 months ago by Devon Ryan1.8k • written 14 months ago by djevo160
2
gravatar for Devon Ryan
14 months ago by
Devon Ryan1.8k
Germany
Devon Ryan1.8k wrote:

Below is an example:

<label id="random_label" text="A big label above the differential expression stuff" />
<section id="some_id" name="NGS: Differential Expression">
  <label id="cufflinks_label" text="Cufflinks stuff" />
  <tool stuff_goes_here />
  <label id="deseq_label" text="DESeq2 stuff" />
  <tool different_stuff_goes_here />
</section>

So, there's a section with a label above it. Inside of that are additional labels

ADD COMMENTlink modified 14 months ago • written 14 months ago by Devon Ryan1.8k

Here is what I have, but it only generates a label called null above the tools in the section.

<section id="hts:_rna_analysis" name="HTS: RNA Analysis" version="">
  <label id= "mapping" name="Mapping"/>
  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/tophat2/758594ed0364/tophat2/tophat2_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.0">
      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
        <repository_name>tophat2</repository_name>
        <repository_owner>devteam</repository_owner>
        <installed_changeset_revision>758594ed0364</installed_changeset_revision>
        <id>toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.0</id>
        <version>2.1.0</version>
    </tool>
</section>
ADD REPLYlink written 14 months ago by djevo160

It seems galaxy is placing the labels above the incorrect tools. I am not sure why this is happening as the mapping programs are listed above cufflinks.

<?xml version="1.0"?>
<toolbox tool_path="../shed_tools">
<section id="hts:_rna_analysis" name="HTS: RNA Analysis" version="">
  <label id= "mapping" text="Mapping" />
  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/tophat2/758594ed0364/tophat2/tophat2_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.0">
      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
        <repository_name>tophat2</repository_name>
        <repository_owner>devteam</repository_owner>
        <installed_changeset_revision>758594ed0364</installed_changeset_revision>
        <id>toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.0</id>
        <version>2.1.0</version>
    </tool>
  <tool file="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/1eb21dccc2fa/hisat2/hisat2.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3">
      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
        <repository_name>hisat2</repository_name>
        <repository_owner>iuc</repository_owner>
        <installed_changeset_revision>1eb21dccc2fa</installed_changeset_revision>
        <id>toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3</id>
        <version>2.0.3</version>
    </tool>
  <tool file="toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/ace9f5a2b40f/rgrnastar/rg_rnaStar.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.4.0d-2">
      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
        <repository_name>rgrnastar</repository_name>
        <repository_owner>iuc</repository_owner>
        <installed_changeset_revision>ace9f5a2b40f</installed_changeset_revision>
        <id>toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.4.0d-2</id>
        <version>2.4.0d-2</version>
    </tool>
  <label id= "cuff_diff" text="Cufflinks" />
  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/b77178f66fc3/cuffcompare/cuffcompare_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/2.2.1.0">
      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
        <repository_name>cuffcompare</repository_name>
        <repository_owner>devteam</repository_owner>
        <installed_changeset_revision>b77178f66fc3</installed_changeset_revision>
        <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/2.2.1.0</id>
        <version>2.2.1.0</version>
    </tool>
  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/986b63735a5e/cuffquant/cuffquant_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/cuffquant/2.2.1.0">
      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
        <repository_name>cuffquant</repository_name>
        <repository_owner>devteam</repository_owner>
        <installed_changeset_revision>986b63735a5e</installed_changeset_revision>
        <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/cuffquant/2.2.1.0</id>
        <version>2.2.1.0</version>
    </tool>
  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/8160c8ea4eb9/cuffmerge/cuffmerge_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.0">
      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
        <repository_name>cuffmerge</repository_name>
        <repository_owner>devteam</repository_owner>
        <installed_changeset_revision>8160c8ea4eb9</installed_changeset_revision>
        <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.0</id>
        <version>2.2.1.0</version>
    </tool>
ADD REPLYlink written 14 months ago by djevo160

It appears that galaxy is parsing the tool conf file in reverse so that the tool at the bottom is the highest on the list.

ADD REPLYlink written 14 months ago by djevo160
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