annotate STACKS_clone_filter.xml @ 9:89b911668f1d draft

planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty

<tool id="STACKS_clone_filter" name="STACKS: clone_filter" version="0.9.0">
  <description>Run the STACKS clone_filter program</description>


<requirements>
    <requirement type="package" version="1.18">stacks</requirement>
</requirements>

<stdio>
   <exit_code range="1" level="fatal" description="Error in Stacks clone_filter" />
</stdio>

<command interpreter="python">
STACKS_clone_filter.py
#if $data_type.dt_select == 'single':
  -f $data_type.fname
#else
  -fwd $data_type.fwd
  -rev $data_type.rev
#end if
  -opt $oligo_option
#if $oligo_len_1 > -1:
  --oligo_len_1 $oligo_len_1
#end if
#if $oligo_len_2 > -1:
  --oligo_len_2 $oligo_len_2
#end if
</command>

<inputs>
    <conditional name="data_type">
      <param name="dt_select" type="select" label="Single or Paired-end">
          <option value="single">Single</option>
          <option value="pair">Pair</option>
      </param>
      <when value="single">
          <param name="fname" type="data" format="fastq" label="FASTQ" />
      </when>
      <when value="pair">
          <param name="fwd" type="data" format="fastq" label="Forward FASTQ" />
          <param name="rev" type="data" format="fastq" label="Reverse FASTQ" />
      </when>
  </conditional>
  <param name="oligo_len_1" value="-1" type="integer" label="length of the single-end oligo sequence in data set (-1 == ignore)"/>
  <param name="oligo_len_2" value="-1" type="integer" label="length of the paired-end oligo sequence in data set (-1 == ignore)"/>
  <param name="oligo_options" type="select" label="Oligo sequence options">
      <option value="inline_null" selected="true">random oligo is inline with sequence, occurs only on single-end read</option>
      <option value="null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option>
      <option value="index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option>
      <option value="inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option>
      <option value="index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option>
      <option value="inline_index">random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header</option>
      <option value="index_inline">random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data)</option>
  </param>
</inputs>

<outputs>
    <data format="fastq" name="clean" from_work_dir="job_outputs/clean.fq">
        <filter>data_type['dt_select'] == 'single' </filter>
    </data>
    <data format="fastq" name="clean_fwd" from_work_dir="job_outputs/fwd.fq">
        <filter>data_type['dt_select'] == 'pair' </filter>
    </data>
    <data format="fastq" name="clean_rev" from_work_dir="job_outputs/rev.fq">
        <filter>data_type['dt_select'] == 'pair' </filter>
    </data>
</outputs>

<tests>
    <test>
        <param name="dt_select" value="pair" />
        <param name="fwd" value="fwd.fq" />
        <param name="rev" value="rev.fq" />
        <output name="clean_fwd" />
        <output name="clean_rev" />
    </test>
</tests>

<help>
--------

**Project links:**

`STACKS website &lt;http://creskolab.uoregon.edu/stacks/&gt;`_ .

`STACKS manual &lt;http://creskolab.uoregon.edu/stacks/stacks_manual.pdf&gt;`_ .

`STACKS google group &lt;https://groups.google.com/forum/#!forum/stacks-users&gt;`_ .

</help>
<citations>
    <citation type="doi">10.1111/mec.12354</citation>
    <citation type="doi">10.1111/mec.12330</citation>
    <citation type="doi">10.1534/g3.111.000240</citation>
    <citation type="doi">10.1534/genetics.111.127324</citation>
    <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation>
    <citation type="doi">10.1073/pnas.1006538107</citation>
</citations>
</tool>