diff DigestorMotif.xml @ 0:d2ba97751d56 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/DigestorMotif.xml	Wed Mar 01 12:43:51 2017 -0500
@@ -0,0 +1,92 @@
+<?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 CTD2Galaxy.-->
+<!--Proposed Tool Section: [Utilities]-->
+<tool id="DigestorMotif" name="DigestorMotif" version="2.1.0">
+  <description>digests a protein database in-silico</description>
+  <macros>
+    <token name="@EXECUTABLE@">DigestorMotif</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>DigestorMotif
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_missed_cleavages:
+  -missed_cleavages $param_missed_cleavages
+#end if
+#if $param_mass_accuracy:
+  -mass_accuracy $param_mass_accuracy
+#end if
+#if $param_min_length:
+  -min_length $param_min_length
+#end if
+#if $param_out_option:
+  -out_option $param_out_option
+#end if
+#if $param_enzyme:
+  -enzyme $param_enzyme
+#end if
+#if $param_motif:
+  -motif     "$param_motif"
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="fasta" optional="False" label="FASTA input file" help="(-in) "/>
+    <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="1" label="the number of allowed missed cleavages" help="(-missed_cleavages) "/>
+    <param name="param_mass_accuracy" type="integer" value="1000" label="give your mass accuracy in pp" help="(-mass_accuracy) "/>
+    <param name="param_min_length" type="integer" value="6" label="minimum length of peptide" help="(-min_length) "/>
+    <param name="param_out_option" type="integer" value="1" label="indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)" help="(-out_option) "/>
+    <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
+      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
+      <option value="unspecific cleavage">unspecific cleavage</option>
+      <option value="Formic_acid">Formic_acid</option>
+      <option value="CNBr">CNBr</option>
+      <option value="Lys-C">Lys-C</option>
+      <option value="Trypsin" selected="true">Trypsin</option>
+      <option value="Arg-C">Arg-C</option>
+      <option value="proline endopeptidase">proline endopeptidase</option>
+      <option value="2-iodobenzoate">2-iodobenzoate</option>
+      <option value="Lys-C/P">Lys-C/P</option>
+      <option value="V8-DE">V8-DE</option>
+      <option value="leukocyte elastase">leukocyte elastase</option>
+      <option value="Trypsin/P">Trypsin/P</option>
+      <option value="Chymotrypsin">Chymotrypsin</option>
+      <option value="V8-E">V8-E</option>
+      <option value="Asp-N">Asp-N</option>
+      <option value="PepsinA">PepsinA</option>
+      <option value="no cleavage">no cleavage</option>
+      <option value="Asp-N_ambic">Asp-N_ambic</option>
+      <option value="TrypChymo">TrypChymo</option>
+    </param>
+    <param name="param_motif" type="text" size="30" value="M" label="the motif for the restricted peptidome" help="(-motif) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <expand macro="advanced_options">
+      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="idxml"/>
+  </outputs>
+  <help>digests a protein database in-silico
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_DigestorMotif.html</help>
+</tool>