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changeset 2:c5085b1ad596 draft

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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/snipfinder commit a770ce682054f35fe7508c80b252bbe2bef68ac2
author chrisd
date Fri, 05 Aug 2016 11:30:58 -0400
parents d612ce3827b9
children 6f5acfac16bf
files snipfinder.xml test-data/sampe_result test-data/samse_best_result test-data/samse_result tool_dependencies.xml variant_caller.xml
diffstat 6 files changed, 83 insertions(+), 94 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snipfinder.xml	Fri Aug 05 11:30:58 2016 -0400
@@ -0,0 +1,60 @@
+<tool id="snipfinder" name="snipfinder" version="0.1.0">
+    <description>A simple naive metagenomics variant caller</description>
+    <requirements>
+        <requirement type="package" version="0.1">snipfinder</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+	metasnp
+	    -amr_fp $reference
+	    #if $sam_type.mode == "single_end"
+	    -samse $sam_type.samse_input
+	    $sam_type.best
+	    #else
+	    -sampe $sam_type.sampe_input
+	    $sam_type.best
+	    #end if
+	    -out_fp $output
+    ]]></command>
+    <inputs>
+	<param type="data" name="reference" format="fasta" label="Reference sequence"/>
+	<conditional name="sam_type">
+	    <param name="mode" type="select" label="SAM file type">
+	        <option value="single_end"></option>
+		<option value="paired_end"></option>
+	    </param>
+	    <when value="single_end">
+	        <param type="data" name="samse_input" format="sam" label="Single-end SAM file"/>
+		<param name="best" type="boolean" label="Filter on unique alignments" truevalue="-b" falsevalue=""/>
+	    </when>
+	    <when value="paired_end">
+		<param type="data" name="sampe_input" format="sam" label="Paired-end SAM file"/>
+		<param name="best" type="boolean" label="Filter on unique alignments" truevalue="-b" falsevalue=""/>
+	    </when>
+	</conditional>
+    </inputs>
+    <outputs>
+	<data name="output" format="tabular" />
+    </outputs>
+    <tests>
+	<test>
+	    <param name="mode" value="single_end"/>
+            <param name="reference" value="ref.fa"/>
+            <param name="samse_input" value="samse.sam"/>
+            <output name="output" file="samse_result" ftype="tabular"/>
+        </test>
+	<test>
+	    <param name="mode" value="paired_end"/>
+	    <param name="reference" value="ref.fa"/>
+	    <param name="sampe_input" value="sampe.sam"/>
+	    <output name="output" file="sampe_result" ftype="tabular"/>
+	</test>
+    </tests>
+    <help><![CDATA[
+
+    ]]></help>
+    <citations>
+    </citations>
+</tool>
--- a/test-data/sampe_result	Thu Jun 30 02:39:23 2016 -0400
+++ b/test-data/sampe_result	Fri Aug 05 11:30:58 2016 -0400
@@ -1,8 +1,10 @@
-Gene,Haplotype Pattern,Occurrence
-chr2:172936693-172938111,1052T->G:1084C->A:1102G->C:,1
-chr2:172936693-172938111,119A->C:126A->C:466T->G:496A->T:,1
-chr2:172936693-172938111,135A->C:138C->G:,1
-chr2:172936693-172938111,273T->A:666G->C:,1
-chr2:172936693-172938111,409A->C:415A->C:799T->G:,1
-chr2:172936693-172938111,589T->G:595T->G:,1
-chr2:172936693-172938111,715C->G:748T->A:,1
+Gene	Haplotype Pattern	Occurrence
+chr2:172936693-172938111	1052T->G:1084C->A:1102G->C	1
+chr2:172936693-172938111	1151A->T:743C->G	1
+chr2:172936693-172938111	119A->C:126A->C:466T->G:496A->T	1
+chr2:172936693-172938111	135A->C:138C->G	1
+chr2:172936693-172938111	273T->A:666G->C	1
+chr2:172936693-172938111	409A->C:415A->C:799T->G	1
+chr2:172936693-172938111	589T->G:595T->G	1
+chr2:172936693-172938111	715C->G:748T->A	1
+chr2:172936693-172938111	96A->C	1
--- a/test-data/samse_best_result	Thu Jun 30 02:39:23 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-Gene,Haplotype Pattern,Occurrence
--- a/test-data/samse_result	Thu Jun 30 02:39:23 2016 -0400
+++ b/test-data/samse_result	Fri Aug 05 11:30:58 2016 -0400
@@ -1,9 +1,9 @@
-Gene,Haplotype Pattern,Occurrence
-chr2:172936693-172938111,1181C->A:1190G->C:,1
-chr2:172936693-172938111,1263T->G:1304A->T:1309A->T:,1
-chr2:172936693-172938111,213T->A:242T->A:257T->A:,1
-chr2:172936693-172938111,469G->T:474T->A:,1
-chr2:172936693-172938111,51T->A:74G->T:114G->T:,1
-chr2:172936693-172938111,671A->T:,1
-chr2:172936693-172938111,737T->A:,1
-chr2:172936693-172938111,949A->C:,1
+Gene	Haplotype Pattern	Occurrence
+chr2:172936693-172938111	114G->T:51T->A:74G->T	1
+chr2:172936693-172938111	1181C->A:1190G->C	1
+chr2:172936693-172938111	1263T->G:1304A->T:1309A->T	1
+chr2:172936693-172938111	213T->A:242T->A:257T->A	1
+chr2:172936693-172938111	469G->T:474T->A	1
+chr2:172936693-172938111	671A->T	1
+chr2:172936693-172938111	737T->A	1
+chr2:172936693-172938111	949A->C	1
--- a/tool_dependencies.xml	Thu Jun 30 02:39:23 2016 -0400
+++ b/tool_dependencies.xml	Fri Aug 05 11:30:58 2016 -0400
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="snp_caller" version="0.1">
+    <package name="snipfinder" version="0.1">
         <install version="1.0">
             <actions>
-                <action type="shell_command">git clone --recursive https://github.com/ChrisD11/snp_caller.git</action>
+                <action type="shell_command">git clone --recursive https://github.com/cdeanj/snipfinder.git</action>
                 <action type="shell_command">make</action>
                 <action type="move_file">
-                    <source>snp</source>
+                    <source>snipfinder</source>
                     <destination>$INSTALL_DIR/bin</destination>
                 </action>
                 <action type="set_environment">
@@ -14,6 +14,6 @@
                 </action>
             </actions>
         </install>
-        <readme>Compiling snp finder requires a C++ compiler</readme>
+        <readme>Compiling snipfinder requires a C++ compiler</readme>
     </package>
 </tool_dependency>
--- a/variant_caller.xml	Thu Jun 30 02:39:23 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-<tool id="snp_caller" name="Snip Finder" version="0.1.0">
-    <description>Identifies snips for both single-end and paired-end data</description>
-    <requirements>
-        <requirement type="package" version="0.1">snp_caller</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command><![CDATA[
-	snp
-	    -amr_fp $reference
-	    #if $sam_type.mode == "single_end"
-	    -samse $sam_type.samse_input
-	    $sam_type.best
-	    #else
-	    -sampe $sam_type.sampe_input
-	    $sam_type.best
-	    #end if
-	    -out_fp $result
-    ]]></command>
-    <inputs>
-	<param type="data" name="reference" format="fasta" label="Reference sequence"/>
-	<conditional name="sam_type">
-	    <param name="mode" type="select" label="SAM file type">
-	        <option value="single_end"></option>
-		<option value="paired_end"></option>
-	    </param>
-	    <when value="single_end">
-	        <param type="data" name="samse_input" format="sam" label="Single-end SAM file"/>
-		<param name="best" type="boolean" label="Filter on unique alignments" truevalue="-b" falsevalue=""/>
-	    </when>
-	    <when value="paired_end">
-		<param type="data" name="sampe_input" format="sam" label="Paired-end SAM file"/>
-		<param name="best" type="boolean" label="Filter on unique alignments" truevalue="-b" falsevalue=""/>
-	    </when>
-	</conditional>
-    </inputs>
-    <outputs>
-	<data name="result" format="tabular" />
-    </outputs>
-    <tests>
-	<test>
-	    <param name="mode" value="single_end"/>
-            <param name="reference" value="ref.fa"/>
-            <param name="samse_input" value="samse.sam"/>
-            <output name="result" file="samse_result" ftype="tabular"/>
-        </test>
-	<test>
-	    <param name="mode" value="paired_end"/>
-	    <param name="reference" value="ref.fa"/>
-	    <param name="sampe_input" value="sampe.sam"/>
-	    <output name="result" file="sampe_result" ftype="tabular"/>
-	</test>
-    </tests>
-    <help><![CDATA[
-This program parses a SAM file and looks for single nucleotide polymorphisms (SNPs). In single-end mode, only alignments with bit four not set are considered. In paired-end mode, only reads that mapped in a proper pair are considered. When filtering on unique alignments, only alignments with the XT:A:U field are considered.
-
-Program: snpfinder
-
-Contact: Chris Dean <cdean11@rams.colostate.edu>
-
-Usage: snp [options]
-
-Options:
-    -amr_fp	amr database path
-    -samse	single-end sam file path
-    -sampe	paired-end sam file path
-    -b		filter on unique alignments
-    ]]></help>
-    <citations>
-    </citations>
-</tool>