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changeset 10:b3427b77073e draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 19:50:46 -0400
parents 54c7e3593aac
children
files mascot.xml mascot_to_pepxml.xml repository_dependencies.xml tool_dependencies.xml
diffstat 4 files changed, 295 insertions(+), 320 deletions(-) [+]
line wrap: on
line diff
--- a/mascot.xml	Sun Mar 29 18:17:54 2015 -0400
+++ b/mascot.xml	Tue Oct 20 19:50:46 2015 -0400
@@ -1,249 +1,230 @@
-<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.1.0">
+<tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.1.1">
+    <description>Mascot MS/MS Search</description>
+    <requirements>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+    </requirements>
+    <command>mascot_search.rb 
+
+        #if $database.source_select=="built_in":
+            -d $database.dbkey
+        #else 
+            -d $database.custom_db
+        #end if
+
+        -f $fragment_ion_tol 
+        -S $server $input_file 
+        -o $output
+        -r
+        ## Variable Mods
+
+        --var-mods='
+        $variable_mods
+        '
+        --fix-mods='
+        $fixed_mods
+        '
+
+        --allowed-charges='$allowed_charges'
+        --enzyme=$enzyme 
+        --instrument='$instrument'
+        -p $precursor_ion_tol
+        --precursor-ion-tol-units=$precursor_tolu 
+
+        #if $email
+            --email=$email 
+        #end if
+
+        -v $missed_cleavages
+
+        #if str ( $quant_method ) != 'No Quant'
+            --quantitation='$quant_method'
+        #end if
+
+        #if $security.security_use
+            --use-security
+            --username $security.username
+            --password $security.password
+        #end if
+
+        #if $proxy
+            --proxy $proxy
+        #end if
+
+        --timeout=600
+
+    </command>
+    <inputs>
+        <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/>
+
+        <conditional name="database">
+            <param name="source_select" type="select" label="Database Type">
+                <option value="built_in">Built-In</option>
+                <option selected="true" value="custom_defined">Custom</option>
+            </param>
+            <when value="built_in">
+                <param name="dbkey" type="select" format="text" >
+                    <label>Database</label>
+                    <options from_file="mascot_databases.loc">
+                        <column name="name" index="0" />
+                        <column name="value" index="2" />
+                    </options>
+                </param>
+            </when>
+            <when value="custom_defined">
+                <param name="custom_db" type="text" size="80" value="SwissProt" label="Database Name" help="Exact name of a database defined on the Mascot server (case-sensitive)"/>
+            </when>
+        </conditional>
 
-	<requirements>
-            <container type="docker">iracooke/protk-1.4.1</container>
-	    <requirement type="package" version="1.4">protk</requirement>
-   </requirements>
+        <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed">
+            <options from_file="mascot_mods.loc">
+                <column name="name" index="0" />
+                <column name="value" index="2" />
+            </options>
+        </param>
+
+        <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed">
+            <options from_file="mascot_mods.loc">
+                <column name="name" index="0" />
+                <column name="value" index="2" />
+            </options>
+        </param>
+
+        <param name="missed_cleavages" type="select" format="text">
+            <label>Missed Cleavages Allowed</label>
+            <option value="0">0</option>
+            <option value="1">1</option>
+            <option selected="true" value="2">2</option>
+        </param>
 
-	<description>Mascot MS/MS Search</description>
+        <param name="enzyme" type="select" format="text">
+            <label>Enzyme</label>
+            <option selected="true" value="Trypsin">Trypsin</option>
+            <option value="Trypsin/P">Trypsin/P</option>
+            <option value="Arg-C">Arg-C</option>
+            <option value="Asp-N">Asp-N</option>
+            <option value="Asp-N_ambic">Asp-N_ambic</option>
+            <option value="Chymotrypsin">Chymotrypsin</option>
+            <option value="CNBr">CNBr</option>
+            <option value="CNBr+Trypsin">CNBr+Trypsin</option>
+            <option value="Formic_acid">Formic_acid</option>
+            <option value="Lys-C">Lys-C</option>
+            <option value="Lys-C/P">Lys-C/P</option>
+               <option value="LysC+AspN">LysC+AspN</option>
+               <option value="Lys-N">Lys-N</option>
+               <option value="PepsinA">PepsinA</option>
+               <option value="semiTrypsin">semiTrypsin</option>
+               <option value="TrypChymo">TrypChymo</option>
+               <option value="TrypsinMSIPI">TrypsinMSIPI</option>
+               <option value="TrypsinMSIPI/P">TrypsinMSIPI/P</option>
+               <option value="V8-DE">V8-DE</option>
+               <option value="V8-E">V8-E</option>
+               <option value="none">none</option>
+        </param>
+
+        <param name="allowed_charges" type="select" format="text">
+            <label>Peptide Charge</label>
+            <option value="8-">8-</option>
+            <option value="7-">7-</option>
+            <option value="6-">6-</option>
+            <option value="5-">5-</option>
+            <option value="4-">4-</option>
+            <option value="3-">3-</option>
+            <option value="2-,3- and 4-">2-,3- and 4-</option>
+            <option value="2- and 3-">2- and 3-</option>
+            <option value="2-">2-</option>
+            <option value="1-,2- and 3-">1-,2- and 3-</option>
+            <option value="1-">1-</option>
+            <option value="Mr">Mr</option>
+            <option value="1+">1+</option>
+            <option value="1+, 2+ and 3+">1+,2+ and 3+</option>
+            <option value="2+">2+</option>
+            <option value="2+ and 3+">2+ and 3+</option>
+            <option selected="true" value="2+,3+ and 4+">2+,3+ and 4+</option>
+            <option value="3+">3+</option>
+            <option value="4+">4+</option>
+            <option value="5+">5+</option>
+            <option value="6+">6+</option>
+            <option value="7+">7+</option>
+            <option value="8+">8+</option>
+        </param>
+
+        <param name="instrument" type="select" format="text">
+            <label>Instrument</label>
+            <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option>
+            <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option>
+            <option selected="true" value="ESI-TRAP">ESI-TRAP</option>
+            <option value="ESI-QUAD">ESI-QUAD</option>
+            <option value="ESI-FTICR">ESI-FTICR</option>
+            <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option>
+            <option value="ESI-4SECTOR">ESI-4SECTOR</option>
+            <option value="FTMS-ECD">FTMS-ECD</option>
+            <option value="ETD-TRAP">ETD-TRAP</option>
+            <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option>
+            <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option>
+            <option value="MALDI-ISD">MALDI-ISD</option>
+            <option value="CID+ETD">CID+ETD</option>
+        </param>
 
 
-	<command>mascot_search.rb 
-
-		#if $database.source_select=="built_in":
-		-d $database.dbkey
-		#else 
-		-d $database.custom_db
-		#end if
-
-		-f $fragment_ion_tol 
-
-		-S $server $input_file 
-
-		-o $output 
-
-		-r
-		
-		## Variable Mods
-
-		--var-mods='
-		$variable_mods
-		'
-		
-		--fix-mods='
-		$fixed_mods
-		'
-
-		--allowed-charges='$allowed_charges'
-
-		--enzyme=$enzyme 
-
-		--instrument='$instrument'
-
-		-p $precursor_ion_tol
-		
-		--precursor-ion-tol-units=$precursor_tolu 
-
-		#if $email
-		--email=$email 
-		#end if
-
-		-v $missed_cleavages
-
-		--quantitation='$quant_method'
-
-		#if $security.security_use
-		--use-security
-		--username $security.username
-		--password $security.password
-		#end if
-
-		#if $proxy
-		--proxy $proxy
-		#end if
-
-		--timeout=600
-
-	</command>
-
-	<inputs>
-	
-    <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/>
-
-	<conditional name="database">
-		<param name="source_select" type="select" label="Database Type">
-			<option value="built_in">Built-In</option>
-			<option selected="true" value="custom_defined">Custom</option>
-		</param>
-		<when value="built_in">
-			<param name="dbkey" type="select" format="text" >
-				<label>Database</label>
-				<options from_file="mascot_databases.loc">
-					<column name="name" index="0" />
-					<column name="value" index="2" />
-				</options>
-			</param>
-		</when>
-		<when value="custom_defined">
-			<param name="custom_db" type="text" size="80" value="SwissProt" label="Database Name" help="Exact name of a database defined on the Mascot server (case-sensitive)"/>
-		</when>
-	</conditional>
-
-	<param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed">
-		<options from_file="mascot_mods.loc">
-			<column name="name" index="0" />
-			<column name="value" index="2" />
-		</options>
-	</param>		
+        <param name="quant_method" type="select" format="text">
+            <label>Quantitation</label>
+            <option selected="true" value="No Quant">No Quant</option>
+            <option value="iTRAQ 4plex">iTRAQ 4plex</option>
+            <option value="iTRAQ 4plex (protein)">iTRAQ 4plex (protein)</option>
+            <option value="iTRAQ 8plex">iTRAQ 8plex</option>
+            <option value="TMT 6plex">TMT 6plex</option>
+            <option value="TMT 2plex">TMT 2plex</option>
+            <option value="DiLeu 4plex">DiLeu 4plex</option>
+            <option value="18O multiplex">18O multiplex</option>
+            <option value="SILAC K+6 R+6 multiplex">SILAC K+6 R+6 multiplex</option>
+            <option value="IPTL (Succinyl and IMID) multiplex">IPTL (Succinyl and IMID) multiplex</option>
+            <option value="ICPL duplex pre-digest [MD]">ICPL duplex pre-digest [MD]</option>
+            <option value="ICPL duplex post-digest [MD]">ICPL duplex post-digest [MD]</option>
+            <option value="ICPL triplex pre-digest [MD]">ICPL triplex pre-digest [MD]</option>
+            <option value="ICPL quadruplex pre-digest [MD]">ICPL quadruplex pre-digest [MD]</option>
+            <option value="18O corrected [MD]">18O corrected [MD]</option>
+            <option value="15N Metabolic [MD]">15N Metabolic [MD]</option>
+            <option value="15N + 13C Metabolic [MD]">15N + 13C Metabolic [MD]</option>
+            <option value="SILAC K+6 R+10 [MD]">SILAC K+6 R+10 [MD]</option>
+            <option value="SILAC K+6 R+10 Arg-Pro [MD]">SILAC K+6 R+10 Arg-Pro [MD]</option>
+            <option value="SILAC K+6 R+6 [MD]">SILAC K+6 R+6 [MD]</option>
+            <option value="SILAC R+6 R+10 [MD]">SILAC R+6 R+10 [MD]</option>
+            <option value="SILAC K+8 R+10 [MD]">SILAC K+8 R+10 [MD]</option>        
+            <option value="SILAC K+4 K+8 R+6 R+10 [MD]">SILAC K+4 K+8 R+6 R+10 [MD]</option>
+            <option value="ICAT ABI Cleavable [MD]">ICAT ABI Cleavable [MD]</option>
+            <option value="ICAT D8 [MD]">ICAT D8 [MD]</option>
+            <option value="Dimethylation [MD]">Dimethylation [MD]</option>
+            <option value="NBS Shimadzu [MD]">NBS Shimadzu [MD]</option>
+            <option value="Acetylation [MD]">Acetylation [MD]</option>
+            <option value="Label-free [MD]">Label-free [MD]</option>
+        </param>
+        <param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.5" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
 
-	<param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed">
-		<options from_file="mascot_mods.loc">
-			<column name="name" index="0" />
-			<column name="value" index="2" />
-		</options>
-	</param>
-	
-	<param name="missed_cleavages" type="select" format="text">
-		<label>Missed Cleavages Allowed</label>
-	    <option value="0">0</option>		
-		<option value="1">1</option>
-		<option selected="true" value="2">2</option>
-	</param>
-	
-	<param name="enzyme" type="select" format="text">
-	    <label>Enzyme</label>
-	    <option selected="true" value="Trypsin">Trypsin</option>
-	    <option value="Trypsin/P">Trypsin/P</option>
-	    <option value="Arg-C">Arg-C</option>
-	    <option value="Asp-N">Asp-N</option>
-	    <option value="Asp-N_ambic">Asp-N_ambic</option>
-	    <option value="Chymotrypsin">Chymotrypsin</option>
-	    <option value="CNBr">CNBr</option>
-	    <option value="CNBr+Trypsin">CNBr+Trypsin</option>
-	    <option value="Formic_acid">Formic_acid</option>
-	    <option value="Lys-C">Lys-C</option>
-	    <option value="Lys-C/P">Lys-C/P</option>
-	   	<option value="LysC+AspN">LysC+AspN</option>
-	   	<option value="Lys-N">Lys-N</option>
-	   	<option value="PepsinA">PepsinA</option>
-	   	<option value="semiTrypsin">semiTrypsin</option>
-	   	<option value="TrypChymo">TrypChymo</option>	   	   	
-	   	<option value="TrypsinMSIPI">TrypsinMSIPI</option>	
-	   	<option value="TrypsinMSIPI/P">TrypsinMSIPI/P</option>
-	   	<option value="V8-DE">V8-DE</option>
-	   	<option value="V8-E">V8-E</option>
-	   	<option value="none">none</option>	   	
-	</param>
-	
-	<param name="allowed_charges" type="select" format="text">
-	    <label>Peptide Charge</label>
-		<option value="8-">8-</option>
-		<option value="7-">7-</option>
-		<option value="6-">6-</option>
-		<option value="5-">5-</option>
-		<option value="4-">4-</option>
-		<option value="3-">3-</option>
-		<option value="2-,3- and 4-">2-,3- and 4-</option>
-		<option value="2- and 3-">2- and 3-</option>
-		<option value="2-">2-</option>
-		<option value="1-,2- and 3-">1-,2- and 3-</option>
-		<option value="1-">1-</option>
-		<option value="Mr">Mr</option>
-		<option value="1+">1+</option>
-	    <option value="1+, 2+ and 3+">1+,2+ and 3+</option>		
-		<option value="2+">2+</option>
-		<option value="2+ and 3+">2+ and 3+</option>
-		<option selected="true" value="2+,3+ and 4+">2+,3+ and 4+</option>
-		<option value="3+">3+</option>
-		<option value="4+">4+</option>
-		<option value="5+">5+</option>
-		<option value="6+">6+</option>
-		<option value="7+">7+</option>
-		<option value="8+">8+</option>
-	</param>
-	
-	<param name="instrument" type="select" format="text">
-	    <label>Instrument</label>
-		<option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option>
-		<option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option>
-		<option selected="true" value="ESI-TRAP">ESI-TRAP</option>
-		<option value="ESI-QUAD">ESI-QUAD</option>
-		<option value="ESI-FTICR">ESI-FTICR</option>
-	    <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option>
-		<option value="ESI-4SECTOR">ESI-4SECTOR</option>
-		<option value="FTMS-ECD">FTMS-ECD</option>
-		<option value="ETD-TRAP">ETD-TRAP</option>
-		<option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option>
-		<option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option>
-		<option value="MALDI-ISD">MALDI-ISD</option>
-		<option value="CID+ETD">CID+ETD</option>
-	</param>
+        <param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/>
+        <param name="precursor_tolu" type="select" format="text">
+            <label>Precursor Ion Tolerance Units</label>
+            <option value="ppm">ppm</option>
+            <option value="Da">Da</option>
+        </param>
+
+        <param name="server" type="text" label="URL to the cgi directory on the Mascot Server " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>
+        <param name="proxy" type="text" label="Proxy Server URL including proxy port" size="60" value="" help="eg http://proxy.latrobe.edu.au:8080"/>
 
-
-	<param name="quant_method" type="select" format="text">
-	    <label>Quantitation</label>
-		<option selected="true" value="None">None</option>
-		<option value="iTRAQ 4plex">iTRAQ 4plex</option>
-		<option value="iTRAQ 4plex (protein)">iTRAQ 4plex (protein)</option>
-		<option value="iTRAQ 8plex">iTRAQ 8plex</option>
-		<option value="TMT 6plex">TMT 6plex</option>
-		<option value="TMT 2plex">TMT 2plex</option>
-	    <option value="DiLeu 4plex">DiLeu 4plex</option>
-		<option value="18O multiplex">18O multiplex</option>
-		<option value="SILAC K+6 R+6 multiplex">SILAC K+6 R+6 multiplex</option>
-		<option value="IPTL (Succinyl and IMID) multiplex">IPTL (Succinyl and IMID) multiplex</option>
-		<option value="ICPL duplex pre-digest [MD]">ICPL duplex pre-digest [MD]</option>
-		<option value="ICPL duplex post-digest [MD]">ICPL duplex post-digest [MD]</option>
-		<option value="ICPL triplex pre-digest [MD]">ICPL triplex pre-digest [MD]</option>
-		<option value="ICPL quadruplex pre-digest [MD]">ICPL quadruplex pre-digest [MD]</option>
-		<option value="18O corrected [MD]">18O corrected [MD]</option>
-		<option value="15N Metabolic [MD]">15N Metabolic [MD]</option>
-		<option value="15N + 13C Metabolic [MD]">15N + 13C Metabolic [MD]</option>
-		<option value="SILAC K+6 R+10 [MD]">SILAC K+6 R+10 [MD]</option>
-		<option value="SILAC K+6 R+10 Arg-Pro [MD]">SILAC K+6 R+10 Arg-Pro [MD]</option>
-		<option value="SILAC K+6 R+6 [MD]">SILAC K+6 R+6 [MD]</option>
-		<option value="SILAC R+6 R+10 [MD]">SILAC R+6 R+10 [MD]</option>
-		<option value="SILAC K+8 R+10 [MD]">SILAC K+8 R+10 [MD]</option>		
-		<option value="SILAC K+4 K+8 R+6 R+10 [MD]">SILAC K+4 K+8 R+6 R+10 [MD]</option>
-		<option value="ICAT ABI Cleavable [MD]">ICAT ABI Cleavable [MD]</option>
-		<option value="ICAT D8 [MD]">ICAT D8 [MD]</option>
-		<option value="Dimethylation [MD]">Dimethylation [MD]</option>
-		<option value="NBS Shimadzu [MD]">NBS Shimadzu [MD]</option>
-		<option value="Acetylation [MD]">Acetylation [MD]</option>
-		<option value="Label-free [MD]">Label-free [MD]</option>
-	</param>	
-	
-	<param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.5" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
-
-	<param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/>
-	<param name="precursor_tolu" type="select" format="text">
-	    <label>Precursor Ion Tolerance Units</label>
-	    <option value="ppm">ppm</option>		
-		<option value="Da">Da</option>
-	</param>
-
-	<param name="server" type="text" label="URL to the cgi directory on the Mascot Server " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>
-	<param name="proxy" type="text" label="Proxy Server URL including proxy port" size="60" value="" help="eg http://proxy.latrobe.edu.au:8080"/>
-
-	<conditional name="security">
-		<param name="security_use" type="boolean" label="Use Mascot Security?" help="Select this if you need to enter a username and password" truevalue="true" falsevalue="false" />
-		<when value="false" />
-		<when value="true">
-			<param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>
-			<param name="password" type="text" label="Password" size="60" value="" help="Mascot Password. Password is encrypted when over the internet but is stored in clear-text on the Galaxy server"/>
-		</when>
-	</conditional>
-	<param name="email" type="text" label="Email " size="60" value="" help=""/>
-	
-	
-
-  </inputs>
-  <outputs>
-    <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database.dbkey if $database.has_key('dbkey') else $database.custom_db}.${input_file.display_name}.mascotdat"/>
-  </outputs>
-
-  <help>
-	Run a Mascot MS/MS Ion Search
-  </help>
-
+        <conditional name="security">
+            <param name="security_use" type="boolean" label="Use Mascot Security?" help="Select this if you need to enter a username and password" truevalue="true" falsevalue="false" />
+            <when value="false" />
+            <when value="true">
+                <param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>
+                <param name="password" type="text" label="Password" size="60" value="" help="Mascot Password. Password is encrypted when over the internet but is stored in clear-text on the Galaxy server"/>
+            </when>
+        </conditional>
+        <param name="email" type="text" label="Email " size="60" value="" help=""/>
+    </inputs>
+    <outputs>
+        <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database.dbkey if $database.has_key('dbkey') else $database.custom_db}.${input_file.display_name}.mascotdat"/>
+    </outputs>
+    <help>
+        Run a Mascot MS/MS Ion Search
+    </help>
 </tool>
--- a/mascot_to_pepxml.xml	Sun Mar 29 18:17:54 2015 -0400
+++ b/mascot_to_pepxml.xml	Tue Oct 20 19:50:46 2015 -0400
@@ -1,83 +1,72 @@
-<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.1.0">
-	<requirements>
-            <container type="docker">iracooke/protk-1.4.1</container>
-	    	<requirement type="package" version="1.4">protk</requirement>
-			<requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
-   </requirements>
+<tool id="mascot_to_pepxml_1" name="Mascot to pepXML" version="1.1.1">
+    <description>Converts a mascot results file to pepXML</description>
+    <requirements>
+        <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
+    </requirements>
+    <command>mascot_to_pepxml.rb 
+        $input_file 
 
-  <description>Converts a mascot results file to pepXML</description>
-
-<command>mascot_to_pepxml.rb 
-	$input_file 
-
-	-o $output 
+        -o $output 
 
-	#if $database.source_select=="built_in":
-	-d $database.dbkey
-	#else 
-	-d $database.fasta_file
-	#end if
+        #if $database.source_select=="built_in":
+            -d $database.dbkey
+        #else 
+            -d $database.fasta_file
+        #end if
 
-	#if $explicit_enzyme.explicit_enzyme_use
-	--enzyme $explicit_enzyme.enzyme
-	#end if
-
-	$shortid
+        #if $explicit_enzyme.explicit_enzyme_use
+            --enzyme $explicit_enzyme.enzyme
+        #end if
 
-</command>
-<inputs>
-
-
-	<param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/>
+        $shortid
+    </command>
+    <inputs>
+        <param name="input_file" type="data" format="mascotdat" multiple="false" label="Input File" help="Mascot results file"/>
 
-	<conditional name="database">
-		<param name="source_select" type="select" label="Database source" help="A local copy of the database used in the Mascot search">
-			<option value="built_in">Built-In</option>
-			<option value="input_ref">Uploaded fasta file</option>
-		</param>
-		<when value="built_in">
-			<param name="dbkey" type="select" format="text" >
-				<label>Database</label>
-				<options from_file="pepxml_databases.loc">
-					<column name="name" index="0" />
-					<column name="value" index="2" />
-				</options>
-			</param>
-		</when>
-		<when value="input_ref">
-			<param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
-		</when>
-	</conditional>
+        <conditional name="database">
+            <param name="source_select" type="select" label="Database source" help="A local copy of the database used in the Mascot search">
+                <option value="built_in">Built-In</option>
+                <option value="input_ref">Uploaded fasta file</option>
+            </param>
+            <when value="built_in">
+                <param name="dbkey" type="select" format="text" >
+                    <label>Database</label>
+                    <options from_file="pepxml_databases.loc">
+                        <column name="name" index="0" />
+                        <column name="value" index="2" />
+                    </options>
+                </param>
+            </when>
+            <when value="input_ref">
+                <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
+            </when>
+        </conditional>
 
-	<param name="shortid" type="boolean" label="Short ID" help="Use protein id from the Mascot result file instead reading from the fasta database." truevalue="--shortid" falsevalue="" />
+        <param name="shortid" type="boolean" label="Short ID" help="Use protein id from the Mascot result file instead reading from the fasta database." truevalue="--shortid" falsevalue="" />
 
-	<conditional name="explicit_enzyme">
-		<param name="explicit_enzyme_use" type="boolean" label="Specify Enzyme" help="If left unchecked the Enzyme will be read from the input file" truevalue="true" falsevalue="false" />
-		<when value="false" />
-		<when value="true">
-			<param name="enzyme" type="text" label="Enzyme" size="80" value="trypsin" help="Semi-cleavage can be specified as semisample_enyzme eg semitrypsin"/>
-		</when>
-	</conditional>
-
-
-
-</inputs>
-<outputs>
-	<data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
-</outputs>
+        <conditional name="explicit_enzyme">
+            <param name="explicit_enzyme_use" type="boolean" label="Specify Enzyme" help="If left unchecked the Enzyme will be read from the input file" truevalue="true" falsevalue="false" />
+            <when value="false" />
+            <when value="true">
+                <param name="enzyme" type="text" label="Enzyme" size="80" value="trypsin" help="Semi-cleavage can be specified as semisample_enyzme eg semitrypsin"/>
+            </when>
+        </conditional>
 
-	<tests>
-    	<test>
-    		<param name="source_select" value="input_ref"/>
-	      	<param name="fasta_file" value="bsa.fasta"/>
-   		   	<param name="input_file" value="F002832.dat"/>
-      		<output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" /> 
-    	</test>
-    	
-  	</tests>
-
-<help>
-	Convert mascot results from mascotdat to pepXML
-</help>
-
+    </inputs>
+    <outputs>
+        <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="source_select" value="input_ref"/>
+              <param name="fasta_file" value="bsa.fasta"/>
+                  <param name="input_file" value="F002832.dat"/>
+              <output name="output" file="bsa_mascot2xml.pep.xml" compare="sim_size" delta="600" />
+        </test>
+    </tests>
+    <help>
+        Convert mascot results from mascotdat to pepXML
+    </help>
 </tool>
--- a/repository_dependencies.xml	Sun Mar 29 18:17:54 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Proteomics datatypes">
-    <repository changeset_revision="ac51d9dbfb4d" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
- </repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 20 19:50:46 2015 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="protk" version="1.4.3">
+        <repository changeset_revision="74bf855be117" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="trans_proteomic_pipeline" version="4.8.0">
+        <repository changeset_revision="a7273394d858" name="package_tpp_4_8_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>