Sub groups within galaxy shed tool conf file

2.1 years ago by

Devon Ryan • 1.9k

Germany

Devon Ryan • 1.9k 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 COMMENT • link modified 2.1 years ago • written 2.1 years ago by Devon Ryan • 1.9k

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 REPLY • link written 2.1 years ago by djevo1 • 60

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 REPLY • link written 2.1 years ago by djevo1 • 60

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 REPLY • link written 2.1 years ago by djevo1 • 60

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