view reverse.seqs.xml @ 2:503898f17f42 draft

planemo upload for repository commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:55:28 -0400
parents a8a1a7c5ab14
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<tool profile="16.07" id="mothur_reverse_seqs" name="Reverse.seqs" version="@WRAPPER_VERSION@.0">
    <description>Reverse complement the sequences</description>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>

## create symlinks to input datasets
ln -s '$fasta' fasta.dat &&

echo 'reverse.seqs(
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
        <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to reverse complement"/>
        <expand macro="param-savelog"/>
        <expand macro="logfile-output"/>
        <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.rc.*" label="${} on ${on_string}: rc.fasta"/>
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
            <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>


**Command Documentation**

The reverse.seqs_ command will generate a fasta containing the reverse complement of each sequence in the input fasta.

.. _reverse.seqs:

    <expand macro="citations"/>