diff OpenSwathDecoyGenerator.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

--- a/OpenSwathDecoyGenerator.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/OpenSwathDecoyGenerator.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,59 +1,111 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="1.12.0">
-  <description>Generates decoys according to different models for a specific TraML</description>
-  <macros>
-    <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>OpenSwathDecoyGenerator
+<?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: [Targeted Experiments]-->
+  <tool id="OpenSwathDecoyGenerator" name="OpenSwathDecoyGenerator" version="2.0.0">
+    <description>Generates decoys according to different models for a specific TraML</description>
+    <macros>
+      <token name="@EXECUTABLE@">OpenSwathDecoyGenerator</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>OpenSwathDecoyGenerator
 
--in ${param_in}
--out ${param_out}
--method ${param_method}
--decoy_tag ${param_decoy_tag}
-${param_theoretical}
--mz_threshold ${param_mz_threshold}
-${param_exclude_similar}
--similarity_threshold ${param_similarity_threshold}
-${param_append}
-${param_remove_CNterm_mods}
-${param_remove_unannotated}
-${param_enable_losses}
--identity_threshold ${param_identity_threshold}
--max_attempts ${param_max_attempts}
--mz_shift ${param_mz_shift}
--precursor_mass_shift ${param_precursor_mass_shift}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_method:
+  -method     &quot;$param_method&quot;
+#end if
+#if $param_decoy_tag:
+  -decoy_tag     &quot;$param_decoy_tag&quot;
+#end if
+#if $param_theoretical:
+  -theoretical
+#end if
+#if $param_mz_threshold:
+  -mz_threshold $param_mz_threshold
+#end if
+#if $param_exclude_similar:
+  -exclude_similar
+#end if
+#if $param_similarity_threshold:
+  -similarity_threshold $param_similarity_threshold
+#end if
+#if $param_append:
+  -append
+#end if
+#if $param_remove_CNterm_mods:
+  -remove_CNterm_mods
+#end if
+#if $param_remove_unannotated:
+  -remove_unannotated
+#end if
+#if $param_enable_losses:
+  -enable_losses
+#end if
+#if $param_identity_threshold:
+  -identity_threshold $param_identity_threshold
+#end if
+#if $param_max_attempts:
+  -max_attempts $param_max_attempts
+#end if
+#if $param_mz_shift:
+  -mz_shift $param_mz_shift
+#end if
+#if $param_precursor_mass_shift:
+  -precursor_mass_shift $param_precursor_mass_shift
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#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="" optional="False" label="input file ('traML')" help="(-in)"/>
-    <param name="param_method" type="text" size="20" value="shuffle" label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" help="(-method)"/>
-    <param name="param_decoy_tag" type="text" size="20" value="DECOY_" label="decoy tag" help="(-decoy_tag)"/>
-    <param name="param_theoretical" type="boolean" truevalue="-theoretical true" falsevalue="-theoretical false" checked="false" optional="True" label="set this flag if only annotated transitions should be used and be corrected to the theoretical mz." help="(-theoretical)"/>
-    <param name="param_mz_threshold" type="float" value="0.05" label="MZ threshold in Thomson for fragment ion annotation" help="(-mz_threshold)"/>
-    <param name="param_exclude_similar" type="boolean" truevalue="-exclude_similar true" falsevalue="-exclude_similar false" checked="false" optional="True" label="set this flag if decoy assays with similarity of the peptide sequence to the target assays higher than the identity_threshold should be excluded. If similarity_threshold is over 0, decoy assays with an absolute difference of the decoy and target product mz smaller than similarity_threshold are further excluded." help="(-exclude_similar)"/>
-    <param name="param_similarity_threshold" type="float" value="-1.0" label="Similarity threshold for absolute difference of the product mz of target and decoy assays for exclusion in Dalton. Suggested value: 0.05" help="(-similarity_threshold)"/>
-    <param name="param_append" type="boolean" truevalue="-append true" falsevalue="-append false" checked="false" optional="True" label="set this flag if non-decoy TraML should be appended to the output." help="(-append)"/>
-    <param name="param_remove_CNterm_mods" type="boolean" truevalue="-remove_CNterm_mods true" falsevalue="-remove_CNterm_mods false" checked="false" optional="True" label="set this flag to remove decoy peptides with C/N terminal modifications (may be necessary depending on the decoy generation method)." help="(-remove_CNterm_mods)"/>
-    <param name="param_remove_unannotated" type="boolean" truevalue="-remove_unannotated true" falsevalue="-remove_unannotated false" checked="false" optional="True" label="set this flag if target assays with unannotated ions should be ignored from decoy generation." help="(-remove_unannotated)"/>
-    <param name="param_enable_losses" type="boolean" truevalue="-enable_losses true" falsevalue="-enable_losses false" checked="false" optional="True" label="set this flag if fragment ions should also be annotated with neutral losses." help="(-enable_losses)"/>
-    <param name="param_identity_threshold" type="float" value="0.7" label="shuffle: identity threshold for the shuffle algorithm" help="(-identity_threshold)"/>
-    <param name="param_max_attempts" type="integer" value="10" label="shuffle: maximum attempts to lower the sequence identity between target and decoy for the shuffle algorithm" help="(-max_attempts)"/>
-    <param name="param_mz_shift" type="float" value="20.0" label="shift: MZ shift in Thomson for shift decoy method" help="(-mz_shift)"/>
-    <param name="param_precursor_mass_shift" type="float" value="0.0" label="Mass shift to apply to the precursor ion" help="(-precursor_mass_shift)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output file" format="data"/>
-  </outputs>
-  <help>**What it does**
-
-Generates decoys according to different models for a specific TraML
+    <inputs>
+      <param format="traml" help="(-in) " label="input file ('traML')" name="param_in" optional="False" type="data"/>
+      <param help="(-method) " label="decoy generation method ('shuffle','pseudo-reverse','reverse','shift')" name="param_method" size="30" type="text" value="shuffle">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param help="(-decoy_tag) " label="decoy tag" name="param_decoy_tag" size="30" type="text" value="DECOY_">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param checked="false" falsevalue="" help="(-theoretical) " label="set this flag if only annotated transitions should be used and be corrected to the theoretical mz" name="param_theoretical" optional="True" truevalue="-theoretical" type="boolean"/>
+      <param help="(-mz_threshold) " label="MZ threshold in Thomson for fragment ion annotation" name="param_mz_threshold" type="float" value="0.05"/>
+      <param checked="false" falsevalue="" help="(-exclude_similar) If similarity_threshold is over 0, decoy assays with an absolute difference of the decoy and target product mz smaller than similarity_threshold are further excluded" label="set this flag if decoy assays with similarity of the peptide sequence to the target assays higher than the identity_threshold should be excluded" name="param_exclude_similar" optional="True" truevalue="-exclude_similar" type="boolean"/>
+      <param help="(-similarity_threshold) Suggested value: 0.05" label="Similarity threshold for absolute difference of the product mz of target and decoy assays for exclusion in Dalton" name="param_similarity_threshold" type="float" value="-1.0"/>
+      <param checked="false" falsevalue="" help="(-append) " label="set this flag if non-decoy TraML should be appended to the output" name="param_append" optional="True" truevalue="-append" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-remove_CNterm_mods) " label="set this flag to remove decoy peptides with C/N terminal modifications (may be necessary depending on the decoy generation method)" name="param_remove_CNterm_mods" optional="True" truevalue="-remove_CNterm_mods" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-remove_unannotated) " label="set this flag if target assays with unannotated ions should be ignored from decoy generation" name="param_remove_unannotated" optional="True" truevalue="-remove_unannotated" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-enable_losses) " label="set this flag if fragment ions should also be annotated with neutral losses" name="param_enable_losses" optional="True" truevalue="-enable_losses" type="boolean"/>
+      <param help="(-identity_threshold) " label="shuffle: identity threshold for the shuffle algorithm" name="param_identity_threshold" type="float" value="0.7"/>
+      <param help="(-max_attempts) " label="shuffle: maximum attempts to lower the sequence identity between target and decoy for the shuffle algorithm" name="param_max_attempts" type="integer" value="10"/>
+      <param help="(-mz_shift) " label="shift: MZ shift in Thomson for shift decoy method" name="param_mz_shift" type="float" value="20.0"/>
+      <param help="(-precursor_mass_shift) " label="Mass shift to apply to the precursor ion" name="param_precursor_mass_shift" type="float" value="0.0"/>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="traml" name="param_out"/>
+    </outputs>
+    <help>Generates decoys according to different models for a specific TraML
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDecoyGenerator.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathDecoyGenerator.html</help>
+  </tool>