diff mothur/tools/mothur/make.contigs.xml @ 31:a3eed59297ea

Patches courtesy of Peter Briggs, Bioinformatics Core Facility University of Manchester make.contigs.xml.patch:# make.contigs.xml.patch make.contigs.xml.patch:# make.contigs.xml.patch:# 1. Fix cosmetic typo in <description> (forard -> forward) make.contigs.xml.patch:# 2. Address error due to having 'mismatch' as the name for both an input and an output parameter: make.contigs.xml.patch:# rename output parameter to 'cmismatch' make.contigs.xml.patch:# 3. Remove 'threshold' parameter: make.contigs in mothur doesn't support a 'threshold' parameter metagenomics.py.patch:# metagenomics.py.patch metagenomics.py.patch:# metagenomics.py.patch:# 1. Groups class: names were being taken from the wrong field (affected shhh.flows tool) metagenomics.py.patch:# 2. Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular metagenomics.py.patch:# data uploads being sniffed as this type mothur_wrapper.py.patch:# mothur_wrapper.py.patch mothur_wrapper.py.patch:# mothur_wrapper.py.patch:# 1. Update 'cmd_dict' settings for shhh.flows and shhh.seqs (otherwise these functions will mothur_wrapper.py.patch:# fail on execution) mothur_wrapper.py.patch:# 2. Fix add_option calls defining '--match' and '--mismatch' command line options (otherwise mothur_wrapper.py.patch:# syntax error causes immediate failure) screen.seqs.xml.patch:# screen.seqs.xml.patch screen.seqs.xml.patch:# screen.seqs.xml.patch:# Replace pattern for align.report output file in definiting of 'results' parameter in screen.seqs.xml.patch:# <command> section (otherwise output_alignreport data item is empty). shhh.flows.xml.patch:# shhh.flows.xml.patch shhh.flows.xml.patch:# shhh.flows.xml.patch:# Replace 'format_source' with 'format' for output parameters (otherwise formats are not shhh.flows.xml.patch:# correctly assigned to output datasets) shhh.seqs.xml.patch:# shhh.seqs.xml.patch shhh.seqs.xml.patch:# shhh.seqs.xml.patch:# 1. Fix patterns in --result (in <command> section) for shhh_seqs.fasta and shhh_seqs.names shhh.seqs.xml.patch:# output files (otherwise files are not collected and associated data items are empty) shhh.seqs.xml.patch:# 2. Replace 'format_source' with 'format' for output parameters (otherwise formats are not shhh.seqs.xml.patch:# correctly assigned to output datasets) trim.flows.xml.patch:# trim.flows.xml.patch trim.flows.xml.patch:# trim.flows.xml.patch:# Remove erroneous space from --result definition in <command> section (otherwise causes tool trim.flows.xml.patch:# failure) trim.seqs.xml.patch:# trim.seqs.xml.patch trim.seqs.xml.patch:# trim.seqs.xml.patch:# 1. Remove reference to undefined 'oligo.allvalues' varible in <command> section (otherwise trim.seqs.xml.patch:# causes failure on execution) trim.seqs.xml.patch:# 2. Fix format for input parameter 'names' (format should be 'names' not 'name') trim.seqs.xml.patch:# 3. Add output parameter 'scrap_names' (to ensure consistent collection of all outputs) trim.seqs.xml.patch:# 4. Update --result definition in <command> section to collect both trim.names and scrap.names

--- a/mothur/tools/mothur/make.contigs.xml	Thu May 30 08:59:17 2013 -0500
+++ b/mothur/tools/mothur/make.contigs.xml	Tue Jul 30 09:26:31 2013 -0500
@@ -1,9 +1,9 @@
 <tool id="mothur_make_contigs" name="Make.contigs" version="1.26.0">
- <description>Aligns paired forard and reverse fastq files to contigs as fasta and quality</description>
+ <description>Aligns paired forward and reverse fastq files to contigs as fasta and quality</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='make.contigs'
-  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.contigs\.fasta$:'$fasta,'^\S+\.contigs\.qual$:'$qual,'^\S+\.contigs\.mismatch$:'$mismatch
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.contigs\.fasta$:'$fasta,'^\S+\.contigs\.qual$:'$qual,'^\S+\.contigs\.mismatch$:'$cmismatch
   --outputdir='$logfile.extra_files_path'
   --ffastq=$ffastq
   --rfastq=$rfastq
@@ -33,9 +33,9 @@
   #if $gapextend.__str__ != '':
    --gapextend=$gapextend
   #end if
-  #if $threshold.__str__ != '':
-   --threshold=$threshold
-  #end if
+  ###if $threshold.__str__ != '':
+  ## --threshold=$threshold
+  ###end if
   --processors=8
  </command>
  <inputs>
@@ -71,16 +71,18 @@
   <param name="mismatch" type="integer" value="-1" optional="true" label="mismatch - Pairwise alignment penalty for a mismatch"/>
   <param name="gapopen" type="integer" value="-2" optional="true" label="gapopen - Pairwise alignment penalty for opening a gap"/>
   <param name="gapextend" type="integer" value="-1" optional="true" label="gapextend - Pairwise alignment penalty for extending a gap"/>
+  <!-- make.contigs doesn't support "threshold" option, see http://www.mothur.org/wiki/Make.contigs
   <param name="threshold" type="integer" value="40" optional="true" label="threshold - for quality scores" 
          help="When we are merging the overlapping regions, in the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score below the threshold we eliminate it.">
       <validator type="in_range" message="threshold can't be negative" min="0"/>
   </param>
+  -->
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
   <data format="fasta" name="fasta" label="${tool.name} on ${on_string}: contigs.fasta"/>
   <data format="qual" name="qual" label="${tool.name} on ${on_string}: contigs.qual"/>
-  <data format="txt" name="mismatch" label="${tool.name} on ${on_string}: contigs.mismatch"/>
+  <data format="txt" name="cmismatch" label="${tool.name} on ${on_string}: contigs.mismatch"/>
  </outputs>
  <requirements>
   <requirement type="package" version="1.27">mothur</requirement>