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changeset 2:72d20758ba2c

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final upload
author wolma
date Wed, 11 Feb 2015 09:23:43 -0500
parents a548b3c6ed00
children ba685c655e18
files annotate_variants.xml bamsort.xml cloudmap.xml convert.xml covstats.xml deletion_predictor.xml fileinfo.xml reheader.xml sam_header.xml snap_caller.xml snp_caller_caller.xml snpeff_genomes.xml toolshed_macros.xml varextract.xml vcf_filter.xml
diffstat 15 files changed, 63 insertions(+), 42 deletions(-) [+]
line wrap: on
line diff
--- a/annotate_variants.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/annotate_variants.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,8 +1,9 @@
 <tool id="annotate_variants" name="Variant Annotation">
   <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>
   	mimodd annotate
--- a/bamsort.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/bamsort.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,8 +1,9 @@
 <tool id="bamsort" name="Sort BAM file">
   <description>Sort a BAM file by coordinates (or names) of the mapped reads</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>
 	mimodd sort "$inputfile" -o "$output" --oformat $oformat $by_name
--- a/cloudmap.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/cloudmap.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,8 +1,9 @@
 <tool id="cloudmap_prepare" name="Prepare variant data for mapping">
   <description>with the CloudMap series of tools.</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>
     mimodd cloudmap "$ifile" ${run.mode} 
--- a/convert.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/convert.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,8 +1,9 @@
 <tool id="convert" name="Convert">
   <description>between different sequence data formats</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>
 	mimodd convert 
--- a/covstats.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/covstats.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,8 +1,9 @@
 <tool id="coverage_stats" name="Coverage Statistics">
   <description>Calculate coverage statistics for a BCF file as generated by the Variant Calling tool</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command> 
 	mimodd covstats "$ifile" --ofile "$output_vcf"
--- a/deletion_predictor.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/deletion_predictor.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,8 +1,9 @@
 <tool id="deletion_prediction" name="Deletion Prediction for paired-end data">
   <description>Predicts deletions in one or more aligned read samples based on coverage of the reference genome and on insert sizes</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>
     mimodd delcall
--- a/fileinfo.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/fileinfo.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,8 +1,9 @@
 <tool id="fileinfo" name="Retrieve File Information">
   <description>for supported data formats.</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>
     mimodd info "$ifile" -o "$outputfile" --verbose --oformat $oformat
--- a/reheader.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/reheader.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,9 +1,10 @@
 <tool id="reheader" name="Reheader BAM file">
 
   <description>From a BAM file generate a new file with the original header (if any) replaced or modified by that found in a second SAM file</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>    
     #if ($str($rg.treat_rg) != "ignore" and $str($rg.rginfo.source) == "from_form") or $str($co.treat_co) != "ignore":
--- a/sam_header.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/sam_header.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,8 +1,9 @@
 <tool id="ngs_run_annotation" name="NGS Run Annotation">
   <description>Create a SAM format header from run metadata for sample annotation.</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>
   	mimodd header
--- a/snap_caller.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/snap_caller.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,8 +1,9 @@
 <tool id="read_alignment" name="SNAP Read Alignment">
   <description>Map sequence reads to a reference genome using SNAP</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command> 
 	mimodd snap-batch -s
--- a/snp_caller_caller.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/snp_caller_caller.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,8 +1,9 @@
 <tool id="variant_calling" name="Variant Calling">
   <description>From a reference and aligned reads generate a BCF file with position-specific variant likelihoods and coverage information</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>
 	mimodd varcall
--- a/snpeff_genomes.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/snpeff_genomes.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,8 +1,9 @@
 <tool id="snpeff_genomes" name="List Installed SnpEff Genomes">
   <description>Checks the local SnpEff installation to compile a list of currently installed genomes</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>
   	mimodd snpeff-genomes -o "$outputfile"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolshed_macros.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -0,0 +1,7 @@
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="0.1.5.2">mimodd</requirement>
+    </requirements>
+  </xml>
+</macros>
--- a/varextract.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/varextract.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,8 +1,9 @@
 <tool id="extract_variants" name="Extract Variant Sites">
   <description>from a BCF file</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command> 
 	mimodd varextract "$ifile"
--- a/vcf_filter.xml	Wed Feb 11 08:57:11 2015 -0500
+++ b/vcf_filter.xml	Wed Feb 11 09:23:43 2015 -0500
@@ -1,8 +1,9 @@
 <tool id="vcf_filter" name="VCF Filter">
   <description>Extracts lines from a vcf variant file based on field-specific filters</description>
-  <requirements>
-    <requirement type="package">mimodd</requirement>
-  </requirements>
+  <macros>
+    <import>toolshed_macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command> 
 	mimodd vcf-filter