Mercurial > repos > jjohnson > mothur_toolsuite
changeset 4:5265aa9067e0
set output formats to match input formats
| author | jjohnson |
|---|---|
| date | Wed, 08 Jun 2011 15:02:44 -0500 |
| parents | b849cd7e132a |
| children | e2e2071d2c62 |
| files | mothur/tools/mothur/bin.seqs.xml mothur/tools/mothur/bootstrap.shared.xml mothur/tools/mothur/cluster.fragments.xml mothur/tools/mothur/consensus.seqs.xml mothur/tools/mothur/degap.seqs.xml mothur/tools/mothur/deunique.seqs.xml mothur/tools/mothur/get.groups.xml mothur/tools/mothur/get.lineage.xml mothur/tools/mothur/get.oturep.xml mothur/tools/mothur/get.seqs.xml mothur/tools/mothur/get.sharedseqs.xml mothur/tools/mothur/pre.cluster.xml mothur/tools/mothur/read.otu.xml mothur/tools/mothur/remove.lineage.xml mothur/tools/mothur/remove.seqs.xml mothur/tools/mothur/split.abund.xml mothur/tools/mothur/split.groups.xml mothur/tools/mothur/sub.sample.xml mothur/tools/mothur/trim.seqs.xml mothur/tools/mothur/unique.seqs.xml |
| diffstat | 20 files changed, 26 insertions(+), 206 deletions(-) [+] |
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--- a/mothur/tools/mothur/bin.seqs.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/bin.seqs.xml Wed Jun 08 15:02:44 2011 -0500 @@ -6,7 +6,7 @@ --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:fasta' + --new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:${fasta.ext}' --fasta=$fasta --list=$otu #if $name.__str__ != "None" and len($name.__str__) > 0:
--- a/mothur/tools/mothur/bootstrap.shared.xml Wed Jun 08 14:59:08 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,126 +0,0 @@ -<tool id="mothur_bootstrap_shared" name="Bootstrap.shared" version="1.16.0" force_history_refresh="True"> - <description>Generate a newick trees for dissimilarity among groups</description> - <command interpreter="python"> - #* -98_sq_phylip_amazon.fn.jclass.bootunique.tre -98_sq_phylip_amazon.fn.thetayc.bootunique.tre -98_sq_phylip_amazon.fn.jclass.bootunique.cons.pairs -98_sq_phylip_amazon.fn.jclass.bootunique.cons.tre -98_sq_phylip_amazon.fn.thetayc.bootunique.cons.pairs -98_sq_phylip_amazon.fn.thetayc.bootunique.cons.tre -98_sq_phylip_amazon.fn.jclass.boot0.00.tre -98_sq_phylip_amazon.fn.thetayc.boot0.00.tre -98_sq_phylip_amazon.fn.jclass.boot0.00.cons.pairs -98_sq_phylip_amazon.fn.jclass.boot0.00.cons.tre -98_sq_phylip_amazon.fn.thetayc.boot0.00.cons.pairs -98_sq_phylip_amazon.fn.thetayc.boot0.00.cons.tre - *# - mothur_wrapper.py - --cmd='bootstrap.shared' - --result='^mothur.\S+\.logfile$:'$logfile - --outputdir='$logfile.extra_files_path' - --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.tre)$:tre','^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.cons\.tre)$:tre','^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.cons\.pairs)$:txt' - --READ_cmd='read.otu' - #if $input.source == 'similarity': - --READ_list=$input.otu - #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: - --READ_group='$otu_group' - #end if - #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: - --READ_label='$input.label' - #end if - #elif $input.source == 'shared': - --READ_shared=$input.otu - #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: - --READ_label='$input.label' - #end if - #end if - #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: - --groups=$input.groups - #end if - #if $calc.__str__ != "None" and len($calc.__str__) > 0: - --calc=$calc - #end if - #if int($iters.__str__) > 0: - --iters=$iters - #end if - </command> - <inputs> - <!-- list,group or shared --> - <conditional name="input"> - <param name="source" type="select" label="Generate Heatmap for"> - <option value="similarity">OTU list</option> - <option value="shared">OTU Shared</option> - </param> - <when value="similarity"> - <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> - <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/> - <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - </options> - </param> - <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> - <options from_dataset="otu_group"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> - </options> - </param> - </when> - <when value="shared"> - <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/> - <param name="label" type="select" label="label - OTU Labels" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="unique_value" name="unq_lbl" column="0" /> - </options> - </param> - <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="1"/> - <column name="value" index="1"/> - <filter type="unique_value" name="unq_grp" column="1" /> - </options> - </param> - </when> - </conditional> - <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> - <options from_file="mothur_calculators.loc"> - <column name="mult2" index="2"/> - <column name="name" index="0"/> - <column name="value" index="0"/> - <filter type="static_value" name="mult2" column="2" value="shar" /> - </options> - </param> - <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/> - </inputs> - <outputs> - <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - </outputs> - <requirements> - <requirement type="binary">mothur</requirement> - </requirements> - <tests> - </tests> - <help> -**Mothur Overview** - -Mothur_, initiated by Dr. Patrick Schloss and his software development team -in the Department of Microbiology and Immunology at The University of Michigan, -provides bioinformatics for the microbial ecology community. - -.. _Mothur: http://www.mothur.org/wiki/Main_Page - -**Command Documenation** - -The bootstrap.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. - -.. _bootstrap.shared: http://www.mothur.org/wiki/Bootstrap.shared - - - </help> -</tool>
--- a/mothur/tools/mothur/cluster.fragments.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/cluster.fragments.xml Wed Jun 08 15:02:44 2011 -0500 @@ -25,7 +25,7 @@ </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> + <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" /> </outputs> <requirements>
--- a/mothur/tools/mothur/consensus.seqs.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/consensus.seqs.xml Wed Jun 08 15:02:44 2011 -0500 @@ -15,13 +15,13 @@ #end if --result='^mothur.\S+\.logfile$:'$logfile --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.(((unique|[0-9.]*)\.)?cons\.fasta)$:fasta','^\S+?\.(((unique|[0-9.]*)\.)?cons\.names)$:names','^\S+?\.(((unique|[0-9.]*)\.)?cons\.summary)$:tabular' + --new_datasets='^\S+?\.(((unique|[0-9.]*)\.)?cons\.fasta)$:${fasta.ext}','^\S+?\.(((unique|[0-9.]*)\.)?cons\.names)$:names','^\S+?\.(((unique|[0-9.]*)\.)?cons\.summary)$:tabular' #else --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.cons\.summary$:'$summary,'^\S+\.cons\.fasta$:'$cons_fasta #end if </command> <inputs> - <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin" help="Sequences must be the same length"/> + <param name="fasta" type="data" format="align" label="fasta - Sequences to Bin" help="Sequences must be the same length"/> <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> <conditional name="otu"> <param name="use" type="select" label="Consensus sequence"> @@ -45,7 +45,7 @@ <data format="tabular" name="summary" label="${tool.name} on ${on_string}: cons.summary"> <filter>otu['use'] == 'no'</filter> </data> - <data format="fasta" name="cons_fasta" label="${tool.name} on ${on_string}: cons.fasta"> + <data format_source="fasta" name="cons_fasta" label="${tool.name} on ${on_string}: cons.fasta"> <filter>otu['use'] == 'no'</filter> </data> </outputs>
--- a/mothur/tools/mothur/degap.seqs.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/degap.seqs.xml Wed Jun 08 15:02:44 2011 -0500 @@ -12,7 +12,7 @@ </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> + <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> </outputs> <requirements> <requirement type="binary">mothur</requirement>
--- a/mothur/tools/mothur/deunique.seqs.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/deunique.seqs.xml Wed Jun 08 15:02:44 2011 -0500 @@ -14,7 +14,7 @@ </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> + <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> </outputs> <requirements> <requirement type="binary">mothur</requirement>
--- a/mothur/tools/mothur/get.groups.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/get.groups.xml Wed Jun 08 15:02:44 2011 -0500 @@ -52,7 +52,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> <!-- fix format --> - <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> + <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> <filter>fasta_in != None</filter> </data> <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name">
--- a/mothur/tools/mothur/get.lineage.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/get.lineage.xml Wed Jun 08 15:02:44 2011 -0500 @@ -53,7 +53,7 @@ <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"/> - <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> + <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> <filter>fasta_in != None</filter> </data> <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.group">
--- a/mothur/tools/mothur/get.oturep.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/get.oturep.xml Wed Jun 08 15:02:44 2011 -0500 @@ -7,7 +7,7 @@ --outputdir='$logfile.extra_files_path' #if $as_datasets.__str__ == "yes": --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:fasta','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names' + --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:${fasta.ext}','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names' #end if --fasta=$fasta --list=$otu_list
--- a/mothur/tools/mothur/get.seqs.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/get.seqs.xml Wed Jun 08 15:02:44 2011 -0500 @@ -53,11 +53,11 @@ <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <!-- format should be set to match input --> - <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> + <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> <filter>fasta_in != None</filter> </data> <!-- format should be set to match input --> - <data format="qual" name="qfile_out" label="${tool.name} on ${on_string}: pick.qfile"> + <data format_source="qfile_in" name="qfile_out" label="${tool.name} on ${on_string}: pick.qfile"> <filter>qfile_in != None</filter> </data> <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.names">
--- a/mothur/tools/mothur/get.sharedseqs.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/get.sharedseqs.xml Wed Jun 08 15:02:44 2011 -0500 @@ -23,7 +23,7 @@ #end if #if $fasta.__str__ != "None" and len($fasta.__str__) > 0: --fasta=$fasta - #set datasets = $datasets + ["'^\S+?\.((unique|[0-9.]*)(\S+)\.shared.fasta)$:fasta'"] + #set datasets = $datasets + ["'^\S+?\.((unique|[0-9.]*)(\S+)\.shared.fasta)$:" + $fasta.ext + "'"] #end if #if $output.__str__ != "None" and len($output.__str__) > 0: --output=$output
--- a/mothur/tools/mothur/pre.cluster.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/pre.cluster.xml Wed Jun 08 15:02:44 2011 -0500 @@ -25,7 +25,7 @@ </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: precluster.fasta" /> + <data format_source="fasta" name="fasta_out" label="${tool.name} on ${on_string}: precluster.fasta" /> <data format="names" name="names_out" label="${tool.name} on ${on_string}: precluster.names" /> </outputs> <requirements>
--- a/mothur/tools/mothur/read.otu.xml Wed Jun 08 14:59:08 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -<tool id="mothur_read_otu" name="Read.otu" version="1.16.0" force_history_refresh="True"> - <description>Read OTU list and group to create a shared file</description> - <command interpreter="python"> - mothur_wrapper.py - --cmd='read.otu' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared:'$shared - --outputdir='$logfile.extra_files_path' - #if $show_rabund.value == True: - --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund' - #end if - --list=$otu - --group=$otu_group - #if $label.__str__ != "None" and len($label.__str__) > 0: - --label='$label' - #end if - </command> - <inputs> - <param name="otu" type="data" format="list" label="list - OTU List"/> - <param name="otu_group" type="data" format="groups" label="group - Group file for the OTU List"/> - <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> - <options from_dataset="otu"> - <column name="name" index="0"/> - <column name="value" index="0"/> - </options> - </param> - <param name="show_rabund" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Put Group rabund files in your history"/> - </inputs> - <outputs> - <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" /> - </outputs> - <requirements> - <requirement type="binary">mothur</requirement> - </requirements> - <tests> - </tests> - <help> -**Mothur Overview** - -Mothur_, initiated by Dr. Patrick Schloss and his software development team -in the Department of Microbiology and Immunology at The University of Michigan, -provides bioinformatics for the microbial ecology community. - -.. _Mothur: http://www.mothur.org/wiki/Main_Page - -**Command Documenation** - -The read.otu_ command is called before most of the OTU based mothur commands. It is included here explicitly to allow the creatation of a shared file from OTU list and group files. - -.. _read.otu: http://www.mothur.org/wiki/Read.otu - - </help> -</tool>
--- a/mothur/tools/mothur/remove.lineage.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/remove.lineage.xml Wed Jun 08 15:02:44 2011 -0500 @@ -54,7 +54,7 @@ <!-- fix format --> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"/> - <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> + <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> <filter>fasta_in != None</filter> </data> <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.group">
--- a/mothur/tools/mothur/remove.seqs.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/remove.seqs.xml Wed Jun 08 15:02:44 2011 -0500 @@ -58,14 +58,14 @@ <filter>fasta_in != None</filter> </data> --> - <data format="fasta" metadata_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.${fasta_in.datatype.file_ext}"> + <data format_source="fasta_in" metadata_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.${fasta_in.datatype.file_ext}"> <filter>fasta_in != None</filter> <change_format> <when input="${fasta_in.datatype.file_ext}" value="align" format="align" /> </change_format> </data> <!-- format should be set to match input --> - <data format="qual" name="qfile_out" label="${tool.name} on ${on_string}: pick.qfile"> + <data format_source="qfile_in" name="qfile_out" label="${tool.name} on ${on_string}: pick.qfile"> <filter>qfile_in != None</filter> <change_format> <when input="${qfile_in.datatype.file_ext}" value="qual454" format="qual454" />
--- a/mothur/tools/mothur/split.abund.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/split.abund.xml Wed Jun 08 15:02:44 2011 -0500 @@ -10,10 +10,10 @@ #set datasets = [] #if $as_datasets.__str__ == "yes": --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.fasta)$:fasta','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.groups)$:groups','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.accnos)$:accnos' + --new_datasets='^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.fasta)$:${fasta.ext}','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.groups)$:groups','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.accnos)$:accnos' #end if --fasta=$fasta - #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.fasta)$',$os.path.basename($fasta.__str__)) + ":fasta'"] + #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.fasta)$',$os.path.basename($fasta.__str__)) + ":" + $fasta.ext + "'"] #if $search.type == "list": --list=$search.input #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.list)$',$os.path.basename($search.input.__str__)) + ":list'"]
--- a/mothur/tools/mothur/split.groups.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/split.groups.xml Wed Jun 08 15:02:44 2011 -0500 @@ -6,7 +6,7 @@ --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.(\S+\.fasta)$:fasta','^\S+?\.(\S+\.names)$:names' + --new_datasets='^\S+?\.(\S+\.fasta)$:${fasta.ext}','^\S+?\.(\S+\.names)$:names' --fasta=$fasta --group=$group #if $name.__str__ != "None" and len($name.__str__) > 0:
--- a/mothur/tools/mothur/sub.sample.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/sub.sample.xml Wed Jun 08 15:02:44 2011 -0500 @@ -165,7 +165,7 @@ </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: subsample.fasta"> + <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: subsample.fasta"> <filter>input['format'] == 'fasta'</filter> </data> <data format="list" name="list_out" label="${tool.name} on ${on_string}: subsample.list">
--- a/mothur/tools/mothur/trim.seqs.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/trim.seqs.xml Wed Jun 08 15:02:44 2011 -0500 @@ -37,7 +37,7 @@ $oligo.allfiles #if $oligo.allfiles.value: --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.(\S+\.fasta)$:fasta','^\S+?\.(\S+\.groups)$:groups' + --new_datasets='^\S+?\.(\S+\.fasta)$:${fasta.ext}','^\S+?\.(\S+\.groups)$:groups' #end if #end if #if $qual.add == "yes": @@ -95,11 +95,11 @@ <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format_source="fasta" name="trim_fasta" label="${tool.name} on ${on_string}: trim.fasta"/> - <data format="qual" name="trim_qual" label="${tool.name} on ${on_string}: trim.qual"> + <data format_source="qfile" name="trim_qual" label="${tool.name} on ${on_string}: trim.qual"> <filter>(qual['add'] == 'yes' and len(qual['qfile'].__str__) > 0)</filter> </data> - <data format="fasta" name="scrap_fasta" label="${tool.name} on ${on_string}: scrap.fasta"/> - <data format="qual" name="scrap_qual" label="${tool.name} on ${on_string}: scrap.qual"> + <data format_source="fasta" name="scrap_fasta" label="${tool.name} on ${on_string}: scrap.fasta"/> + <data format_source="qfile" name="scrap_qual" label="${tool.name} on ${on_string}: scrap.qual"> <filter>(qual['add'] == 'yes' and len(qual['qfile'].__str__) > 0)</filter> </data> <data format="groups" name="groups_file" label="${tool.name} on ${on_string}: groups">
--- a/mothur/tools/mothur/unique.seqs.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/unique.seqs.xml Wed Jun 08 15:02:44 2011 -0500 @@ -16,7 +16,7 @@ </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> + <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" /> </outputs> <requirements>