view ctat_concatenate.xml @ 0:702a3586942a draft default tip

Upload ctat tools.
author trinity_ctat
date Tue, 17 Jul 2018 11:48:23 -0400
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<tool id="ctat_concatenate" name="ctat_concatenate" version="1.0.0" profile="17.05">
    <description> concatenate datasets from tail to head</description>
        <requirement type="package" version="2.7">python</requirement>

    <command detect_errors="exit_code">
        python $__tool_directory__/ cat
        #for $q in $queries
        #end for
        > $out_file1 
        <param name="input1" type="data" label="Concatenate Dataset"/>
        <repeat name="queries" title="Dataset">
            <param name="input2" type="data" label="Select" />
        <data name="out_file1" format="input" metadata_source="input1"/>

            <param name="input1" value="Sp_ds.left.fq"/>
            <param name="input2" value="Sp_hs.left.fq"/>
            <output name="out_file1" file="Sp.cat_ds_hs.left.fq">
                    <has_line_matching expression=".+" />
            <param name="input1" value="Sp_ds.right.fq"/>
            <param name="input2" value="Sp_hs.right.fq"/>
            <output name="out_file1" file="Sp.cat_ds_hs.right.fq">
                    <has_line_matching expression=".+" />
        <!--TODO: if possible, enhance the underlying test code to handle this test
            the problem is multiple params with the same name "input2"
            <param name="input1" value="1.bed"/>
            <param name="input2" value="2.bed"/>
            <param name="input2" value="3.bed"/>
            <output name="out_file1" file="cat_wrapper_out2.bed"/>
.. class:: infomark 

Combine left and right reads of paired ends for different conditions into a single target for Trinity assembly.

If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_.

.. _here:
.. _paper: