comparison cherry_pick_fasta.xml @ 6:d8fa616a228a draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit 8384f1bb5378232bbe78319e06a3522674c7c1fe"

5:144b856e926c

<tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="3.2.1">
  <description>with header satisfying a string query</description>
  <requirements>
        <requirement type="package" version="1.75">biopython</requirement>
  </requirements>
  <command interpreter="python">cherry_pick_fasta.py
                                   --input $input
                                   --searchfor '$search.searchfor'
                                   #if $search.options_selector == 'single':
                                       #if $search.match == 'exact':
                                           --query-string '$search.query' --mode exact

                                       #else:
                                           --query-file '$search.query' --mode includes
                                       #end if
                                   #end if
                                   --output $output
  </command>

  <inputs>
    <param name="input" type="data" format="fasta" label="Source file" help="Fasta file to parse" />

    <conditional name="search">

  </inputs>
  <outputs>
    <data name="output" format="fasta" label="Fasta sequences ${search.searchfor.value} ${search.options_selector} term(s) in header" />
  </outputs>
  <tests>
    <!-- exact matches -->
    <test>
        <param ftype="fasta" name="input" value="input.fa" />
        <param name="query" value="gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_65_Transcript_1/2_Confidence_0.667_Length_1344_hit1_IdMatch=43.46,AligLength=451,E-val=2e-122" />
        <param name="searchfor" value="without" />

6:d8fa616a228a

<tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="3.3">
  <description>with header satisfying a string query</description>
  <requirements>
        <requirement type="package" version="3.8.0">python</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
                            python '$__tool_directory__/cherry_pick_fasta.py'
                                   --input $input
                                   --searchfor '$search.searchfor'
                                   #if $search.options_selector == 'single':
                                       #if $search.match == 'exact':
                                           --query-string '$search.query' --mode exact

                                       #else:
                                           --query-file '$search.query' --mode includes
                                       #end if
                                   #end if
                                   --output $output
  ]]></command>

  <inputs>
    <param name="input" type="data" format="fasta" label="Source file" help="Fasta file to parse" />

    <conditional name="search">

  </inputs>
  <outputs>
    <data name="output" format="fasta" label="Fasta sequences ${search.searchfor.value} ${search.options_selector} term(s) in header" />
  </outputs>
  <tests>
    <!-- test headers with space -->
    <test>
        <param ftype="fasta" name="input" value="input_withspace.fa" />
        <param name="query" value="type=rRNA" />
        <param name="searchfor" value="with" />
        <param name="match" value="include" />
        <output name="output" ftype="fasta" file="output_withspace.fa" />
    </test>
    <!-- exact matches -->
    <test>
        <param ftype="fasta" name="input" value="input.fa" />
        <param name="query" value="gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_65_Transcript_1/2_Confidence_0.667_Length_1344_hit1_IdMatch=43.46,AligLength=451,E-val=2e-122" />
        <param name="searchfor" value="without" />