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changeset 15:0faaab4f192a draft

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:47:05 -0400
parents 9d6e0ad4d600
children 63b15b77e56c
files repository_dependencies.xml tandem.xml tandem_to_pepxml.xml tool_dependencies.xml
diffstat 4 files changed, 198 insertions(+), 224 deletions(-) [+]
line wrap: on
line diff
--- a/repository_dependencies.xml	Thu Mar 26 19:53:53 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>
--- a/tandem.xml	Thu Mar 26 19:53:53 2015 -0400
+++ b/tandem.xml	Tue Oct 20 20:47:05 2015 -0400
@@ -1,206 +1,180 @@
-<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.0">
-
+<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.1">
+    <description>Run an X!Tandem Search</description>
    <requirements>
-         <container type="docker">iracooke/protk-1.4.1</container>
-	    <requirement type="package" version="1.4">protk</requirement>
-   </requirements>
-
-	<description>Run an X!Tandem Search</description>
+         <container type="docker">iracooke/protk-1.4.3</container>
+        <requirement type="package" version="1.4.3">protk</requirement>
+    </requirements>
+    <command>
+        #if $database.source_select=="built_in":
+            tandem_search.rb -d $database.dbkey 
+        #else
+            tandem_search.rb -d $database.fasta_file
+        #end if
 
-	<command>
-		#if $database.source_select=="built_in":
-		tandem_search.rb -d $database.dbkey 
-		#else 
-		tandem_search.rb -d $database.fasta_file
-		#end if
-
-		#if $tandem_params.source_select=="built_in":
-		-T $tandem_params.paramskey 
-		#else 
-		-T $tandem_params.params_file
-		#end if
+        #if $tandem_params.source_select=="built_in":
+            -T $tandem_params.paramskey 
+        #else 
+            -T $tandem_params.params_file
+        #end if
 
 
-		--var-mods='
-		$variable_mods
-		#for $custom_variable_mod in $custom_variable_mods:
-		,${custom_variable_mod.custom_mod}
-		#end for
-		'
+        --var-mods='
+        $variable_mods
+        #for $custom_variable_mod in $custom_variable_mods:
+            ,${custom_variable_mod.custom_mod}
+        #end for
+        '
 
-		--fix-mods='
-		$fixed_mods
-		#for $custom_fix_mod in $custom_fix_mods:
-		,${custom_fix_mod.custom_mod}
-		#end for
-		'
-
-		$input_file -o $output -r 
-
-		--enzyme=$enzyme 
+        --fix-mods='
+        $fixed_mods
+        #for $custom_fix_mod in $custom_fix_mods:
+            ,${custom_fix_mod.custom_mod}
+        #end for
+        '
 
-		--precursor-ion-tol-units=$precursor_tolu 
-
-		-v $missed_cleavages 
+        $input_file -o $output -r 
 
-		-f $fragment_ion_tol 
-
-		-p $precursor_ion_tol
-
-		$allow_multi_isotope_search 
+        --enzyme=$enzyme 
 
-		$acetyl_protein_nterm
-
-		$cleavage_semi
-
-		$keep_spectra
-
-		--threads $threads
-		
-	</command>
+        --precursor-ion-tol-units=$precursor_tolu 
+        -v $missed_cleavages 
+        -f $fragment_ion_tol 
+        -p $precursor_ion_tol
+        $allow_multi_isotope_search 
+        $acetyl_protein_nterm
+        $cleavage_semi
+        $keep_spectra
+        --threads "\${GALAXY_SLOTS:-12}"
 
-	<inputs>
-		<conditional name="database">
-			<param name="source_select" type="select" label="Database source">
-				<option value="built_in">Built-In</option>
-				<option value="input_ref" selected="true">Your Upload 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="tandem_params">
-			<param name="source_select" type="select" label="Baseline Parameters">
-				<option value="built_in" selected="true">Built-In</option>
-				<option value="input_ref">Custom parameter file</option>
-			</param>
-			<when value="built_in">
-				<param name="paramskey" type="select" format="text" >
-					<label>Paramset</label>
-					<option value="isb_kscore">ISB K-Score (Recommended for TPP)</option>
-				    <option value="isb_native">ISB Native</option>		
-				    <option value="gpm">GPM</option>
-				</param>
-			</when>
-			<when value="input_ref">
-				<param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
-			</when>
-		</conditional>
+    </command>
+    <inputs>
+        <conditional name="database">
+            <param name="source_select" type="select" label="Database source">
+                <option value="built_in">Built-In</option>
+                <option value="input_ref" selected="true">Your Upload 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="tandem_params">
+            <param name="source_select" type="select" label="Baseline Parameters">
+                <option value="built_in" selected="true">Built-In</option>
+                <option value="input_ref">Custom parameter file</option>
+            </param>
+            <when value="built_in">
+                <param name="paramskey" type="select" format="text" >
+                    <label>Paramset</label>
+                    <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option>
+                    <option value="isb_native">ISB Native</option>
+                    <option value="gpm">GPM</option>
+                </param>
+            </when>
+            <when value="input_ref">
+                <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
+            </when>
+        </conditional>
 
-		<param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A file with MS/MS data"/>
+        <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A file with MS/MS data"/>
 
-		<param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
-			clicking to select multiple items">
-			<options from_file="tandem_mods.loc">
-				<column name="name" index="0" />
-				<column name="value" index="2" />
-			</options>
-		</param>
+        <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
+            clicking to select multiple items">
+            <options from_file="tandem_mods.loc">
+                <column name="name" index="0" />
+                <column name="value" index="2" />
+            </options>
+        </param>
 
-		<repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
-			<param name="custom_mod" type="text">
-			</param>
-		</repeat>
-		
-		
-		<param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
-			clicking to select multiple items">
-			<options from_file="tandem_mods.loc">
-				<column name="name" index="0" />
-				<column name="value" index="2" />
-			</options>
-		</param>
+        <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
+            <param name="custom_mod" type="text">
+            </param>
+        </repeat>
+
+        <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
+            clicking to select multiple items">
+            <options from_file="tandem_mods.loc">
+                <column name="name" index="0" />
+                <column name="value" index="2" />
+            </options>
+        </param>
 
-		<repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
-			<param name="custom_mod" type="text">
-			</param>
-		</repeat>
-
-		<param name="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" />		
-		
+        <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
+            <param name="custom_mod" type="text">
+            </param>
+        </repeat>
 
-		<param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
-			<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="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" />        
+        <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
+            <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="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/>
-
-		<param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>
+        <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/>
+        <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>
 
-		<param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search. Maximum is 16"/>
-		
-		<param name="enzyme" type="select" format="text">
-		    <label>Enzyme</label>
-			<option value="[R]__pc__{P}">argc - [R]|{P}</option>
-			<option value="[X]__pc__[D]">aspn - [X]|[D]</option>
-			<option value="[FLMWY]__pc__{P}">chymotrypsin - [FLMWY]|{P}</option>
-			<option value="[R]__pc__[X]">clostripain - [R]|[X]</option>
-			<option value="[M]__pc__{X}">cnbr - [M]|{X}</option>
-			<option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option>
-			<option value="[D]__pc__{P}">formicacid - [D]|{P}</option>
-			<option value="[DE]__pc__{P}">gluc - [DE]|{P}</option>
-			<option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option>
-			<option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option>
-			<option value="[K]__pc__{P}">lysc - [K]|{P}</option>
-			<option value="[K]__pc__[X]">lysc-p - [K]|[X]</option>
-			<option value="[X]__pc__[K]">lysn - [X]|[K]</option>
-			<option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option>
-			<option value="[X]__pc__[X]">nonspecific - [X]|[X]</option>
-			<option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option>
-			<option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option>
-			<option value="[E]__pc__[X]">staph_protease - [E]|[X]</option>
-			<option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
-			<option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option>
-			<option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
-			<option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
-			<option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option>
-		</param>
+        <param name="enzyme" type="select" format="text">
+            <label>Enzyme</label>
+            <option value="[R]__pc__{P}">argc - [R]|{P}</option>
+            <option value="[X]__pc__[D]">aspn - [X]|[D]</option>
+            <option value="[FLWY]__pc__{P}">chymotrypsin - [FLWY]|{P}</option>
+            <option value="[R]__pc__[X]">clostripain - [R]|[X]</option>
+            <option value="[M]__pc__{X}">cnbr - [M]|{X}</option>
+            <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option>
+            <option value="[D]__pc__{P}">formicacid - [D]|{P}</option>
+            <option value="[DE]__pc__{P}">gluc - [DE]|{P}</option>
+            <option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option>
+            <option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option>
+            <option value="[K]__pc__{P}">lysc - [K]|{P}</option>
+            <option value="[K]__pc__[X]">lysc-p - [K]|[X]</option>
+            <option value="[X]__pc__[K]">lysn - [X]|[K]</option>
+            <option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option>
+            <option value="[X]__pc__[X]">nonspecific - [X]|[X]</option>
+            <option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option>
+            <option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option>
+            <option value="[E]__pc__[X]">staph_protease - [E]|[X]</option>
+            <option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
+            <option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option>
+            <option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
+            <option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
+            <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option>
+        </param>
 
-		
-		<param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>
-
-		<param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
-		<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="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="--multi-isotope-search" falsevalue=""/>
-
-	</inputs>
-
-
-	<outputs>
-		<data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/>
-	</outputs>
-
-	<tests>
-		<!-- Just test that the tool runs and produces vaguely correct output -->
-		<test>
-		    <param name="source_select" value="input_ref"/>
-		    <param name="fasta_file" value="testdb.fasta" format="fasta"/>
-		    <param name="input_file" value="tiny.mzML" format="mzml"/>
-		    <output name="output" format="tandem">
-		        <assert_contents>
-					<has_text text="tandem-style" />
-		        </assert_contents>
-		    </output>
-		</test>
-	</tests>
+        <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>
+        <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
+        <param name="precursor_tolu" type="select" format="text">
+            <label>Precursor Ion Tolerance Units</label>
+            <option value="ppm">ppm</option>
+            <option value="Da">Da</option>
+        </param>
+        <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="--multi-isotope-search" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/>
+    </outputs>
+    <tests>
+        <!-- Just test that the tool runs and produces vaguely correct output -->
+        <test>
+            <param name="source_select" value="input_ref"/>
+            <param name="fasta_file" value="testdb.fasta" format="fasta"/>
+            <param name="input_file" value="tiny.mzML" format="mzml"/>
+            <output name="output" format="tandem">
+                <assert_contents>
+                    <has_text text="tandem-style" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
   <help>
 
 **What it does**
--- a/tandem_to_pepxml.xml	Thu Mar 26 19:53:53 2015 -0400
+++ b/tandem_to_pepxml.xml	Tue Oct 20 20:47:05 2015 -0400
@@ -1,38 +1,33 @@
-<tool id="tandem_to_pepxml_1" name="Tandem 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>
+<tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.1">
+    <description>Converts a tandem result 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>
+        tandem_to_pepxml.rb $input_file -o $output 
+    </command>
 
-	<description>Converts a tandem result file to pepXML</description>
-
-	<command>
-		tandem_to_pepxml.rb $input_file -o $output 
-	</command>
-
-	<inputs>
-		<param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/>
-	</inputs>
+    <inputs>
+        <param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/>
+    </inputs>
 
-	<outputs>
-		<data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
-	</outputs>
-
-	<help>
-		Convert X!Tandem results to pepXML
-	</help>
-
-	<tests>
-		<!-- Just test that the tool runs and produces vaguely correct output -->
-		<test>
-		    <param name="input_file" value="tandem_to_pepxml_test.tandem" format="tandem"/>
-		    <output name="output" format="raw_pepxml">
-		        <assert_contents>
-					<has_text text="SQVFQLESTFDV" />
-		        </assert_contents>
-		    </output>
-		</test>
-	</tests>
-
+    <outputs>
+        <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
+    </outputs>
+    <tests>
+        <!-- Just test that the tool runs and produces vaguely correct output -->
+        <test>
+            <param name="input_file" value="tandem_to_pepxml_test.tandem" format="tandem"/>
+            <output name="output" format="raw_pepxml">
+                <assert_contents>
+                    <has_text text="SQVFQLESTFDV" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+        Convert X!Tandem results to pepXML
+    </help>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 20 20:47:05 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>