comparison protein_blast_grouping.xml @ 1:f2a7dffab581 draft

planemo upload commit 6dde4ec93f27f36a10017393063dcf0568f1d405

0:7abe5f471364

    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive">
    <![CDATA[
      '$__tool_directory__/protein_blast_grouping.py'
      '${blast_in.blast}'
      --hits '$hits'
      --sort '$sort.sortType'
      > '$grouping_output'
    ]]>
  </command>
  <inputs>
    <conditional name="blast_in">
      <param name="blastType" type="select" label="Blastn Input Type">

      </conditional>
      <param name="hits" value="20"/>
      <output name="grouping_output" file="outfile.txt" lines_diff="1"/>
    </test>
  </tests>
  <help>
**What it does**
* Reads a tab-delimited BLAST output file.
* Extracts organism names from the subject titles (text in square brackets).
* Counts unique query proteins that matched each organism and unique hit proteins from each organism.
* Sorts and displays results based on either unique queries or unique hits.
* The output is a formatted table showing the top N organisms with the most matches.
</help>
  <expand macro="citations-2020"/>
</tool>

1:f2a7dffab581

    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive">
    <![CDATA[
      $__tool_directory__/protein_blast_grouping.py
      '${blast_in.blast}'
      --hits '$hits'
      --sort '$sort.sortType'
      --output '$grouping_output'
    ]]>
  </command>
  <inputs>
    <conditional name="blast_in">
      <param name="blastType" type="select" label="Blastn Input Type">

      </conditional>
      <param name="hits" value="20"/>
      <output name="grouping_output" file="outfile.txt" lines_diff="1"/>
    </test>
  </tests>
  <help><![CDATA[
  **What it does**
  * Reads a tab-delimited BLAST output file.
  * Extracts organism names from the subject titles (text in square brackets).
  * Counts unique query proteins that matched each organism and unique hit proteins from each organism.
  * Sorts and displays results based on either unique queries or unique hits.
  * The output is a formatted table showing the top N organisms with the most matches.
  ]]>
</help>
  <expand macro="citations-2020"/>
</tool>