--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RNADigestor.xml	Thu Sep 03 16:14:58 2020 +0000
@@ -0,0 +1,86 @@
+<?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@
+#import re
+
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${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 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_MC1">RNase_MC1</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>
+      <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="Overwrite 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" multiple="true" label="Optional outputs" optional="true">
+      <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>
+    <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/documentation/UTILS_RNADigestor.html]]></help>
+  <expand macro="references"/>
+</tool>