diff snp_caller_caller.xml @ 23:5db0545b9004 draft

update to v0.1.7.3

--- a/snp_caller_caller.xml	Sun Jun 12 07:39:46 2016 -0400
+++ b/snp_caller_caller.xml	Thu Jul 21 03:55:49 2016 -0400
@@ -1,9 +1,9 @@
-<tool id="variant_calling" name="Variant Calling" version="0.1.7.2">
+<tool id="variant_calling" name="Variant Calling" version="0.1.7.3">
   <description>From a reference and aligned reads generate a BCF file with position-specific variant likelihoods and coverage information</description>
   <macros>
     <import>toolshed_macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
+  <expand macro="requirements" />
   <version_command>python3 -m MiModD version -q</version_command>
   <command>
 	python3 -m MiModD varcall
@@ -21,17 +21,17 @@
   </command>
 
   <inputs>
-    <param name="ref_genome" type="data" format="fasta" label="reference genome" />
-    <repeat name="list_input" title="Aligned reads input source" default="1" min="1">
-      <param name="inputfile" type="data" format="bam" label="input file" />
+    <param format="fasta" label="reference genome" name="ref_genome" type="data" />
+    <repeat default="1" min="1" name="list_input" title="Aligned reads input source">
+      <param format="bam" label="input file" name="inputfile" type="data" />
     </repeat>
-    <param name="group_by_id" type="boolean" label="group reads based on read group id only" truevalue="-i" falsevalue="" checked="false" help="If selected, this option ensures that only the read group id (but not the sample name) is considered in grouping reads in the input file(s). If turned off, read groups with identical sample names are automatically pooled and analyzed together even if they come from different NGS runs." />
-    <param name="no_md5_check" type="boolean" label="turn off md5 sum verification" truevalue="-x" falsevalue="" checked="false" help="leave turned on to avoid accidental variant calling against a wrong reference genome version (see the tool help below)." />
-    <param name="depth" type="integer" value="250" label="maximum per-BAM depth (default: 250)" help="to avoid excessive use of memory"/>
+    <param checked="false" falsevalue="" help="If selected, this option ensures that only the read group id (but not the sample name) is considered in grouping reads in the input file(s). If turned off, read groups with identical sample names are automatically pooled and analyzed together even if they come from different NGS runs." label="group reads based on read group id only" name="group_by_id" truevalue="-i" type="boolean" />
+    <param checked="false" falsevalue="" help="leave turned on to avoid accidental variant calling against a wrong reference genome version (see the tool help below)." label="turn off md5 sum verification" name="no_md5_check" truevalue="-x" type="boolean" />
+    <param help="to avoid excessive use of memory" label="maximum per-BAM depth (default: 250)" name="depth" type="integer" value="250" />
   </inputs>
 
   <outputs>
-    <data name="output_vcf" format="bcf" label="Variant Calls from MiModd Variant Calling on ${on_string}"/>
+    <data format="bcf" label="Variant Calls from MiModd Variant Calling on ${on_string}" name="output_vcf" />
   </outputs>
 
 <help>
@@ -63,4 +63,4 @@
 It exposes just a single configuration parameter of these tools - the *maximum per-BAM depth*. Through this parameter, the maximum number of reads considered for variant calling at any site can be controlled. Its default value of 250 is taken from *samtools mpileup* and usually suitable. Consider, however, that this gives the maximum read number per input file, so if you have a large number of samples in one input file, it could become necessary to increase the value to get sufficient reads considered per sample.
 
 </help>
-</tool>
+</tool>
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