<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
<!--Proposed Tool Section: [RNA]-->
<tool id="RNADigestor" name="RNADigestor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Digests an RNA sequence database in-silico</description>
  <macros>
    <token name="@EXECUTABLE@">RNADigestor</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir out &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-out
'out/output.${gxy2omsext("fasta")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("fasta")}' '$out'
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in" type="data" format="fasta" label="Input file containing RNA sequences" help=" select fasta data sets(s)"/>
    <param argument="-missed_cleavages" type="integer" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
    <param argument="-min_length" type="integer" value="3" label="Minimum length of a fragment" help=""/>
    <param argument="-max_length" type="integer" value="30" label="Maximum length of a fragment" help=""/>
    <param argument="-enzyme" type="select" label="Digestion enzyme (RNase)" help="">
      <option value="RNase_T1" selected="true">RNase_T1</option>
      <option value="RNase_H">RNase_H</option>
      <option value="mazF">mazF</option>
      <option value="colicin_E5">colicin_E5</option>
      <option value="RNase_MC1">RNase_MC1</option>
      <option value="RNase_A">RNase_A</option>
      <option value="RNase_U2">RNase_U2</option>
      <option value="cusativin">cusativin</option>
      <option value="no cleavage">no cleavage</option>
      <option value="unspecific cleavage">unspecific cleavage</option>
      <expand macro="list_string_san" name="enzyme"/>
    </param>
    <param argument="-unique" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Report each unique sequence fragment only once" help=""/>
    <param argument="-cdna" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Input file contains cDNA sequences - replace 'T' with 'U')" help=""/>
    <expand macro="adv_opts_macro">
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="fasta"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <test expect_num_outputs="1">
      <!--random RNAsequence input -->
      <param name="adv_opts|test" value="true"/>
      <param name="in" ftype="fasta" value="random_RNA.fa"/>
      <output name="out" ftype="fasta" value="RNADigestor.fasta"/>
    </test>
  </tests>
  <help><![CDATA[Digests an RNA sequence database in-silico.


For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_RNADigestor.html]]></help>
  <expand macro="references"/>
</tool>