view presto_macros.xml @ 3:620f3b0a1430 draft default tip

"planemo upload for repository commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
author iuc
date Sat, 25 Sep 2021 18:34:18 +0000
parents 824d24bfe8dd
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    <xml name="citations">
            <citation type="doi">10.1093/bioinformatics/btu138</citation>
            <yield />
    <xml name="bio_tools">
            <xref type="">presto</xref>
    <token name="@TOOL_VERSION@">0.6.2</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">20.05</token>
    <xml name="requirements">
              <requirement type="package" version="@TOOL_VERSION@">presto</requirement>
    <xml name="presto-coord-param">
        <param argument="--coord" type="select"  value="presto"  label="Coordinate" help="The format of the sequence identifier which defines shared coordinate information across mate pairs.">
            <option value="illumina">Illumina</option>
            <option value="solexa">Solexa</option>
            <option value="sra">SRA</option>
            <option value="454">454</option>
            <option value="presto">pRESTO</option>
    <xml name="presto-log-param">
        <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
    <xml name="presto-log-output">
        <data name="log_out" format="txt" label="Log from ${} on ${on_string}">
    <xml name="text-regex-validator">
        <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[A-Za-z0-9_ ]+</validator>

    <token name="@PRESTO_URL_BASE@"></token>
    <token name="@HELP_NOTE@"><![CDATA[


**Note about limitations of pRESTO tools within Galaxy:**

pRESTO tools in galaxy have the following limitations vs. when run at the command line:

* Inputs must be FASTQ format and cannot be FASTA format.
* Multiple inputs files are not supported per argument (e.g. ``-1``, ``-2`` or ``-s``), i.e.
    - Steps that take a pair of fastq inputs can only take two files, not two sets of files
    - Steps that take a single set of fastq inputs can only take a single file
* The ``--outdir`` and ``--outname`` options are not supported; output files are named directly