comparison mothur/tools/mothur/shhh.flows.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

30:a90d1915a176

      <validator type="in_range" message="large value must be positive" min="1"/>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="fasta" name="shhh_fasta" label="${tool.name} on ${on_string}: shhh.fasta"/>
  <data format_source="qual454" name="shhh_qual" label="${tool.name} on ${on_string}: shhh.qual"/>
  <data format_source="names" name="shhh_names" label="${tool.name} on ${on_string}: shhh.names"/>
  <data format_source="groups" name="shhh_groups" label="${tool.name} on ${on_string}: shhh.groups"/>
  <data format_source="tabular" name="shhh_counts" label="${tool.name} on ${on_string}: shhh.counts"/>
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">mothur</requirement>
 </requirements>
 <tests>

31:a3eed59297ea

      <validator type="in_range" message="large value must be positive" min="1"/>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="fasta" name="shhh_fasta" label="${tool.name} on ${on_string}: shhh.fasta"/>
  <data format="qual454" name="shhh_qual" label="${tool.name} on ${on_string}: shhh.qual"/>
  <data format="names" name="shhh_names" label="${tool.name} on ${on_string}: shhh.names"/>
  <data format="groups" name="shhh_groups" label="${tool.name} on ${on_string}: shhh.groups"/>
  <data format="tabular" name="shhh_counts" label="${tool.name} on ${on_string}: shhh.counts"/>
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">mothur</requirement>
 </requirements>
 <tests>