# HG changeset patch
# User mzeidler
# Date 1380047029 14400
# Node ID d042cf2f4043b93e5e8561d4f1ee9a4ffd42537f
# Parent  312cb1b2d3cd734b8cc61593d3fa8a28e0d9ae4b
Uploaded

diff -r 312cb1b2d3cd -r d042cf2f4043 vmap_dnamap.xml
--- a/vmap_dnamap.xml	Tue Sep 24 14:22:46 2013 -0400
+++ b/vmap_dnamap.xml	Tue Sep 24 14:23:49 2013 -0400
@@ -7,9 +7,7 @@
         <requirement type="package" version="0.1.19">samtools</requirement>
         <requirement type="package" version="0.7.4">bwa</requirement>
         <requirement type="package" version="1.0">virana_python</requirement>
-        <requirement type="package" version="1.7.1">numpy</requirement>
-        <requirement type="package" version="1.61">biopython</requirement>
-        <requirement type="package" version="0.5.4">htseq</requirement>
+
     </requirements>
 
     <command interpreter="python">vmap.py dnamap
@@ -86,24 +84,24 @@
     </command>
     
     <inputs>
-        <param name="reads" type="data" format="fastq" label="Read file"/>
+        <param name="reads" type="data" format="fastq" label="Read file" help="input read file"/>
         
         <conditional name="paired">
-            <param name="select_paired" type="select" label="Paired end reads?" >
+            <param name="select_paired" type="select" label="Paired end reads?" help="Set to 'paired end' in case of paired end read input.">
                 <option value="single">single end</option>
                 <option value="paired">paired end</option>
             </param>
             
            <when value="paired">
-                <param name="paired_read" type="data" format="fastq" label="Paired end read file" />
+                <param name="paired_read" type="data" format="fastq" label="Paired end read file" help="input paired end read file" />
            </when>
         
         </conditional>
         <conditional name="output_type">
-            <param name="hit" type="boolean" label="Hit Output"/>
+            <param name="hit" type="boolean" label="Hit Output" help="check this box for output of virana hit file"/>
                            
             <when value="true">
-                <param name="max_mismatches" type="integer" min="0" max="10000000"  optional="true" label="Maximum number of mismatches for saved hits"/>
+                <param name="max_mismatches" type="integer" min="0" max="10000000"  optional="true" label="Maximum number of mismatches for saved hits" />
                 <param name="max_relative_mismatches" type="float" min="0" max="1" optional="true" label="Maximum number of mismatches relative to read length for saved hits " />
                 <param name="min_continiously_matching" type="integer" min="0" max="10000000" optional="true" label="Minimum number of continious matches for saved hits"  />
                 <param name="min_mapping_score" type="integer" min="1" max="255"  optional="true" label="Mimimum mapping score for saved hit"  />        
@@ -114,12 +112,12 @@
         
         </conditional>
         
-        <param name="bam" type="boolean" label="BAM Output"/>
-        <param name="sam" type="boolean" label="SAM Output"/>
-        <param name="qual" type="boolean"  label="Quality Output"/>
-        <param name="tax" type="boolean"  label="Taxonomy Output"/>
+        <param name="bam" type="boolean" label="BAM Output" help="check this box for output of unsorted, unindexed BAM file"/>
+        <param name="sam" type="boolean" label="SAM Output" help="check this box for output of SAM file"/>
+        <param name="qual" type="boolean"  label="Quality Output" help="check this box  for output of quality file"/>
+        <param name="tax" type="boolean"  label="Taxonomy Output" help="check this box for output of taxonomy file"/>
         
-        <param name="refseq" type="select" label="Set RefSeq taxonomic groups" multiple="true" display="checkboxes" optional="true">
+        <param name="refseq" type="select" label="Set RefSeq taxonomic groups" multiple="true" display="checkboxes" optional="true" help="Only generate hit groups that include at last one read mapping to a reference of this reference group">
             <option value="UniVec">UniVec</option>
             <option value="rRNA">rRNA</option>
             <option value="Homo_sapiens">Homo sapiens</option>
@@ -133,7 +131,7 @@
             <option value="Bacteria_DRAFT">Bacteria DRAFT</option>
         </param>
         
-        <param name="index" type="data" format="bwa_index" label="BWA Index files"/>
+        <param name="index" type="data" format="bwa_index" label="BWA Index files" help="BWA Index files to map the reades against."/>
         
         <param name="sample_id" type="text" optional="true" label="String used to designate sample information within the hit file"/>