comparison RNADigestor.xml @ 4:c951784e4967 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

3:6d492588ae83

<?xml version='1.0' encoding='UTF-8'?>
<!--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: [Utilities]-->
<tool id="RNADigestor" name="RNADigestor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Digests an RNA sequence database in-silico.</description>
  <macros>
    <token name="@EXECUTABLE@">RNADigestor</token>
    <import>macros.xml</import>
    <import>macros_autotest.xml</import>
    <import>macros_test.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@

  <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 name="in" argument="-in" type="data" format="fasta" optional="false" label="Input file containing RNA sequences" help=" select fasta data sets(s)"/>
    <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
    <param name="min_length" argument="-min_length" type="integer" optional="true" value="3" label="Minimum length of a fragment" help=""/>
    <param name="max_length" argument="-max_length" type="integer" optional="true" value="30" label="Maximum length of a fragment" help=""/>
    <param name="enzyme" argument="-enzyme" type="select" optional="false" label="Digestion enzyme (RNase)" help="">
      <option value="RNase_T1" selected="true">RNase_T1</option>
      <option value="RNase_H">RNase_H</option>
      <option value="no cleavage">no cleavage</option>
      <option value="unspecific cleavage">unspecific cleavage</option>
      <option value="cusativin">cusativin</option>
      <option value="RNase_U2">RNase_U2</option>
      <option value="RNase_A">RNase_A</option>
      <option value="RNase_MC1">RNase_MC1</option>
      <expand macro="list_string_san"/>
    </param>
    <param name="unique" argument="-unique" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Report each unique sequence fragment only once" help=""/>
    <param name="cdna" 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 name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san"/>
      </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>

    <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>
    <expand macro="autotest_RNADigestor"/>
    <expand macro="manutest_RNADigestor"/>
  </tests>
  <help><![CDATA[Digests an RNA sequence database in-silico.


For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_RNADigestor.html]]></help>
  <expand macro="references"/>
</tool>

4:c951784e4967

<?xml version='1.0' encoding='UTF-8'?>
<!--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: [Utilities]-->
<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@

  <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" optional="false" label="Input file containing RNA sequences" help=" select fasta data sets(s)"/>
    <param argument="-missed_cleavages" type="integer" optional="true" min="0" value="1" label="The number of allowed missed cleavages" help=""/>
    <param argument="-min_length" type="integer" optional="true" value="3" label="Minimum length of a fragment" help=""/>
    <param argument="-max_length" type="integer" optional="true" value="30" label="Maximum length of a fragment" help=""/>
    <param argument="-enzyme" type="select" optional="true" label="Digestion enzyme (RNase)" help="">
      <option value="RNase_U2">RNase_U2</option>
      <option value="RNase_A">RNase_A</option>
      <option value="RNase_MC1">RNase_MC1</option>
      <option value="RNase_H">RNase_H</option>
      <option value="cusativin">cusativin</option>
      <option value="RNase_T1" selected="true">RNase_T1</option>
      <option value="mazF">mazF</option>
      <option value="colicin_E5">colicin_E5</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" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <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>

    <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 http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNADigestor.html]]></help>
  <expand macro="references"/>
</tool>