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changeset 6:59c6a5729ce0 draft

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planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/coverage_sampler commit 1127fb7751ab1d3feb4273f23ae3cfea304e0961-dirty
author chrisd
date Tue, 28 Jun 2016 22:49:28 -0400
parents 17bce2f348b6
children d43960f50fc1
files README.md coverage_sampler.xml gene_fraction.xml
diffstat 3 files changed, 116 insertions(+), 80 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Tue Jun 28 22:49:28 2016 -0400
@@ -0,0 +1,36 @@
+Coverage Sampler: A simple tool for calculating the amount of a gene that is covered by a sample of alignments.
+
+#### Installation
+```
+git clone https://github.com/cdeanj/coverage_sampler
+cd coverage_sampler
+make
+./csa
+```
+
+#### Usage
+Usage: csa [options]
+
+Options:
+
+    -ref_fp    STR/FILE	    ref file path
+    -sam_fp    STR/FILE	    sam file path
+    -min       INT      	starting sample level
+    -max       INT	        ending sample level
+    -skip      INT	        amount of sample levels to skip
+    -t         INT	        gene fraction threshold
+    -samples   INT	        iterations per sample level
+    -out_fp    STR/FILE	    output file path
+
+#### Output
+
+The output is a tab delimited text file with five columns
+```
+Level   Iteration   Gene Id Gene Fraction   Hits
+```
+
+* Level: the sampling percent alignments were taken at
+* Iteration: the ith iteration of the current sample level
+* Gene Id: the reference sequence having a gene fraction greater than the threshold
+* Gene Fraction: the number of bases covered by the sample of alignments
+* Hits: the number of alignments that had bases cover the reference sequence
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coverage_sampler.xml	Tue Jun 28 22:49:28 2016 -0400
@@ -0,0 +1,80 @@
+<tool id="coverage_sampler" name="Coverage Sampler" version="0.1.0">
+    <description>A simple tool for calculating the amount of a gene that is covered by a sample of alignments</description>
+    <requirements>
+	<requirement type="package" version="0.1">csa</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+	csa
+	  -ref_fp $reference
+	  -sam_fp $sam
+	  -min $min
+	  -max $max
+	  -t $threshold
+	  -skip $skip
+	  -samples $samples
+	  -out_fp $output
+    ]]></command>
+    <inputs>
+	<param type="data" name="reference" format="fasta" label="Reference sequence" />
+	<param type="data" name="sam" format="sam" label="SAM file" />
+	<param name="min" type="integer" label="Starting sample level"
+	       value="1" min="1" max="100" help="(-min)" />
+	<param name="max" type="integer" label="Ending sample level"
+	       value="1" min="1" max="100" help="(-max)" />
+	<param name="threshold" type="integer" label="Gene fraction threshold"
+	       value="0" min="0" max="100" help="(-t)" />
+	<param name="skip" type="integer" label="Amount of sample levels to skip"
+	       value="1" min="1" max="100" help="(-skip)" />
+	<param name="samples" type="integer" label="Iterations per sample level"
+	       value="1" min="1" max="100" help="(-samples)" />
+    </inputs>
+    <outputs>
+	<data name="output" format="tabular" />
+    </outputs>
+    <tests>
+      <test>
+          <param name="reference" value="ref.fa"/>
+      	  <param name="sam" value="sampe.sam"/>
+	  <param name="min" value="100"/>
+	  <param name="max" value="100"/>
+	  <param name="threshold" value="50"/>
+	  <param name="skip" value="5"/>
+	  <param name="samples" value="1"/>
+      	  <output name="output" file="csa_result" ftype="tabular"/>
+      </test>
+      <test>
+	  <param name="reference" value="ref.fa"/>
+          <param name="sam" value="sampe.sam"/>
+          <param name="min" value="100"/>
+          <param name="max" value="100"/>
+          <param name="threshold" value="80"/>
+          <param name="skip" value="5"/>
+          <param name="samples" value="1"/>
+          <output name="output" file="csa_no_result" ftype="tabular"/>
+      </test>
+    </tests>
+    <help><![CDATA[
+A simple tool for calculating the amount of a gene that is covered by a sample of alignments.
+
+Program: Coverage Sampler
+
+Contact: Chris Dean <cdean11@rams.colostate.edu>
+
+Usage: csa [options]
+
+Options:
+    -ref_fp    STR/FILE	    	ref file path
+    -sam_fp    STR/FILE	    	sam file path
+    -min       INT      		starting sample level
+    -max       INT	        	ending sample level
+    -skip      INT	        	amount of sample levels to skip
+    -t         INT	        	gene fraction threshold
+    -samples   INT	        	iterations per sample level
+    -out_fp    STR/FILE	    	output file path
+    ]]></help>
+    <citations>
+    </citations>
+</tool>
--- a/gene_fraction.xml	Tue Jun 28 22:31:53 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-<tool id="gene_fraction" name="Coverage Sampler" version="0.1.0">
-    <description>A simple tool for calculating the amount of a gene that is covered by a sample of reads</description>
-    <requirements>
-	<requirement type="package" version="0.1">csa</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command><![CDATA[
-	csa
-	  -ref_fp $reference
-	  -sam_fp $sam
-	  -min $min
-	  -max $max
-	  -t $threshold
-	  -skip $skip
-	  -samples $samples
-	  -out_fp $output
-    ]]></command>
-    <inputs>
-	<param type="data" name="reference" format="fasta" label="Reference sequence" />
-	<param type="data" name="sam" format="sam" label="SAM file" />
-	<param name="min" type="integer" label="Starting sample level"
-	       value="1" min="1" max="100" help="(-min)" />
-	<param name="max" type="integer" label="Ending sample level"
-	       value="1" min="1" max="100" help="(-max)" />
-	<param name="threshold" type="integer" label="Gene fraction threshold"
-	       value="0" min="0" max="100" help="(-t)" />
-	<param name="skip" type="integer" label="Amount of sample levels to skip"
-	       value="1" min="1" max="100" help="(-skip)" />
-	<param name="samples" type="integer" label="Iterations per sample level"
-	       value="1" min="1" max="100" help="(-samples)" />
-    </inputs>
-    <outputs>
-	<data name="output" format="tabular" />
-    </outputs>
-    <tests>
-      <test>
-          <param name="reference" value="ref.fa"/>
-      	  <param name="sam" value="sampe.sam"/>
-	  <param name="min" value="100"/>
-	  <param name="max" value="100"/>
-	  <param name="threshold" value="50"/>
-	  <param name="skip" value="5"/>
-	  <param name="samples" value="1"/>
-      	  <output name="output" file="csa_result" ftype="tabular"/>
-      </test>
-      <test>
-	  <param name="reference" value="ref.fa"/>
-          <param name="sam" value="sampe.sam"/>
-          <param name="min" value="100"/>
-          <param name="max" value="100"/>
-          <param name="threshold" value="80"/>
-          <param name="skip" value="5"/>
-          <param name="samples" value="1"/>
-          <output name="output" file="csa_no_result" ftype="tabular"/>
-      </test>
-    </tests>
-    <help><![CDATA[
-A simple tool for calculating the amount of a gene that is covered by a sample of alignments.
-
-Program: Coverage Sampler
-
-Contact: Chris Dean <cdean11@rams.colostate.edu>
-
-Usage: csa [options]
-
-Options:
-    -ref_fp    STR/FILE	    ref file path
-    -sam_fp    STR/FILE	    sam file path
-    -min       INT      	starting sample level
-    -max       INT	        ending sample level
-    -skip      INT	        amount of sample levels to skip
-    -t         INT	        gene fraction threshold
-    -samples   INT	        iterations per sample level
-    -out_fp    STR/FILE	    output file path
-    ]]></help>
-    <citations>
-    </citations>
-</tool>