Mercurial > repos > jjohnson > mothur_toolsuite
changeset 4:a9d51d14f9e9 draft
Add tool_dependencies
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mothur/tool_dependencies.xml Wed Sep 05 21:28:43 2012 -0500 @@ -0,0 +1,35 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="mothur" version="1.24.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://www.mothur.org/w/images/0/09/Mothur.1.24.1.zip</action> + <action type="shell_command">cd Mothur.source</action> + <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>mothur</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>uchime</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +These links provide information for building the Mothur package in most environments . + +http://www.mothur.org/wiki/Download_mothur + +http://www.mothur.org/wiki/Installation + +http://www.mothur.org/wiki/Makefile_options + + </readme> + </package> +</tool_dependency> +
--- a/mothur/tools/mothur/align.check.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/align.check.xml Wed Sep 05 21:28:43 2012 -0500 @@ -33,7 +33,7 @@ <data format="align.check" name="out_file" label="${tool.name} on ${on_string}: align.check"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/align.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/align.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -96,7 +96,7 @@ <data format="align.report" name="report" label="${tool.name} on ${on_string}: align.report" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/amova.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/amova.xml Wed Sep 05 21:28:43 2012 -0500 @@ -26,7 +26,7 @@ <data format="tabular" name="amova" label="${tool.name} on ${on_string}: amova"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/anosim.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/anosim.xml Wed Sep 05 21:28:43 2012 -0500 @@ -26,7 +26,7 @@ <data format="tabular" name="anosim" label="${tool.name} on ${on_string}: anosim"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/bin.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/bin.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -34,7 +34,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/bootstrap.shared.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/bootstrap.shared.xml Wed Sep 05 21:28:43 2012 -0500 @@ -1,126 +0,0 @@ -<tool id="mothur_bootstrap_shared" name="Bootstrap.shared" version="1.16.0" force_history_refresh="True"> - <description>Generate a newick trees for dissimilarity among groups</description> - <command interpreter="python"> - #* -98_sq_phylip_amazon.fn.jclass.bootunique.tre -98_sq_phylip_amazon.fn.thetayc.bootunique.tre -98_sq_phylip_amazon.fn.jclass.bootunique.cons.pairs -98_sq_phylip_amazon.fn.jclass.bootunique.cons.tre -98_sq_phylip_amazon.fn.thetayc.bootunique.cons.pairs -98_sq_phylip_amazon.fn.thetayc.bootunique.cons.tre -98_sq_phylip_amazon.fn.jclass.boot0.00.tre -98_sq_phylip_amazon.fn.thetayc.boot0.00.tre -98_sq_phylip_amazon.fn.jclass.boot0.00.cons.pairs -98_sq_phylip_amazon.fn.jclass.boot0.00.cons.tre -98_sq_phylip_amazon.fn.thetayc.boot0.00.cons.pairs -98_sq_phylip_amazon.fn.thetayc.boot0.00.cons.tre - *# - mothur_wrapper.py - --cmd='bootstrap.shared' - --result='^mothur.\S+\.logfile$:'$logfile - --outputdir='$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 ${on_string}: logfile" /> - </outputs> - <requirements> - <requirement type="binary">mothur</requirement> - </requirements> - <tests> - </tests> - <help> -**Mothur Overview** - -Mothur_, initiated by Dr. Patrick Schloss and his software development team -in the Department of Microbiology and Immunology at The University of Michigan, -provides bioinformatics for the microbial ecology community. - -.. _Mothur: http://www.mothur.org/wiki/Main_Page - -**Command Documenation** - -The bootstrap.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. - -.. _bootstrap.shared: http://www.mothur.org/wiki/Bootstrap.shared - - - </help> -</tool>
--- a/mothur/tools/mothur/chimera.bellerophon.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/chimera.bellerophon.xml Wed Sep 05 21:28:43 2012 -0500 @@ -31,7 +31,7 @@ <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: bellerophon.accnos" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.ccode.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/chimera.ccode.xml Wed Sep 05 21:28:43 2012 -0500 @@ -64,7 +64,7 @@ <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: ccode.accnos" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.check.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/chimera.check.xml Wed Sep 05 21:28:43 2012 -0500 @@ -64,7 +64,7 @@ <data format="txt" name="out_file" label="${tool.name} on ${on_string}: chimeracheck.chimeras" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.perseus.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/chimera.perseus.xml Wed Sep 05 21:28:43 2012 -0500 @@ -34,7 +34,7 @@ <data format="tabular" name="out_file" label="${tool.name} on ${on_string}: perseus.chimeras" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.pintail.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/chimera.pintail.xml Wed Sep 05 21:28:43 2012 -0500 @@ -122,7 +122,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.slayer.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/chimera.slayer.xml Wed Sep 05 21:28:43 2012 -0500 @@ -98,7 +98,7 @@ <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: slayer.accnos" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chimera.uchime.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/chimera.uchime.xml Wed Sep 05 21:28:43 2012 -0500 @@ -149,7 +149,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/chop.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/chop.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -26,7 +26,7 @@ <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: chop.fasta" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/classify.otu.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/classify.otu.xml Wed Sep 05 21:28:43 2012 -0500 @@ -85,7 +85,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/classify.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/classify.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -121,7 +121,7 @@ <data format="tax.summary" name="tax_summary" label="${tool.name} on ${on_string}: tax.summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/classify.tree.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/classify.tree.xml Wed Sep 05 21:28:43 2012 -0500 @@ -33,7 +33,7 @@ <data format_source="tabular" name="summary" label="${tool.name} on ${on_string}: taxonomy.summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/clearcut.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/clearcut.xml Wed Sep 05 21:28:43 2012 -0500 @@ -64,7 +64,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/cluster.classic.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/cluster.classic.xml Wed Sep 05 21:28:43 2012 -0500 @@ -54,7 +54,7 @@ <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/cluster.fragments.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/cluster.fragments.xml Wed Sep 05 21:28:43 2012 -0500 @@ -29,7 +29,7 @@ <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/cluster.split.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/cluster.split.xml Wed Sep 05 21:28:43 2012 -0500 @@ -115,7 +115,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/cluster.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/cluster.xml Wed Sep 05 21:28:43 2012 -0500 @@ -72,7 +72,7 @@ <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/collect.shared.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/collect.shared.xml Wed Sep 05 21:28:43 2012 -0500 @@ -85,7 +85,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/collect.single.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/collect.single.xml Wed Sep 05 21:28:43 2012 -0500 @@ -79,7 +79,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/consensus.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/consensus.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -56,7 +56,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/cooccurrence.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/cooccurrence.xml Wed Sep 05 21:28:43 2012 -0500 @@ -61,7 +61,7 @@ <data format="tabular" name="out_summary" label="${tool.name} on ${on_string}: cooccurence.summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/corr.axes.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/corr.axes.xml Wed Sep 05 21:28:43 2012 -0500 @@ -65,7 +65,7 @@ <data format="axes" name="corr_axes" label="${tool.name} on ${on_string}: corr.axes"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/count.groups.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/count.groups.xml Wed Sep 05 21:28:43 2012 -0500 @@ -47,7 +47,7 @@ <data format="tabular" name="grp_count" label="${tool.name} on ${on_string}: group.count" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/count.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/count.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -36,7 +36,7 @@ <data format="tabular" name="seq_count" label="${tool.name} on ${on_string}: seq.count" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/create.database.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/create.database.xml Wed Sep 05 21:28:43 2012 -0500 @@ -38,7 +38,7 @@ <data format="tabular" name="database" label="${tool.name} on ${on_string}: database" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/degap.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/degap.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -15,7 +15,7 @@ <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/deunique.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/deunique.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -17,7 +17,7 @@ <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/deunique.tree.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/deunique.tree.xml Wed Sep 05 21:28:43 2012 -0500 @@ -17,7 +17,7 @@ <data format_source="tree" name="out_tree" label="${tool.name} on ${on_string}: deunique.tre" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/dist.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/dist.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -49,7 +49,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/dist.shared.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/dist.shared.xml Wed Sep 05 21:28:43 2012 -0500 @@ -118,7 +118,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/fastq.info.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/fastq.info.xml Wed Sep 05 21:28:43 2012 -0500 @@ -22,7 +22,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/filter.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/filter.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -57,7 +57,7 @@ <data format="align" name="out_fasta" label="${tool.name} on ${on_string}: filtered fasta" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.group.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/get.group.xml Wed Sep 05 21:28:43 2012 -0500 @@ -15,7 +15,7 @@ <data format="groups" name="bootgroups" label="${tool.name} on ${on_string}: bootGroups" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.groups.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/get.groups.xml Wed Sep 05 21:28:43 2012 -0500 @@ -94,7 +94,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.lineage.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/get.lineage.xml Wed Sep 05 21:28:43 2012 -0500 @@ -73,7 +73,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.otulist.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/get.otulist.xml Wed Sep 05 21:28:43 2012 -0500 @@ -38,7 +38,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.oturep.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/get.oturep.xml Wed Sep 05 21:28:43 2012 -0500 @@ -90,7 +90,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.otus.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/get.otus.xml Wed Sep 05 21:28:43 2012 -0500 @@ -55,7 +55,7 @@ <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.rabund.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/get.rabund.xml Wed Sep 05 21:28:43 2012 -0500 @@ -30,7 +30,7 @@ <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.relabund.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/get.relabund.xml Wed Sep 05 21:28:43 2012 -0500 @@ -42,7 +42,7 @@ <data format="relabund" name="relabund" label="${tool.name} on ${on_string}: relabund" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.sabund.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/get.sabund.xml Wed Sep 05 21:28:43 2012 -0500 @@ -27,7 +27,7 @@ <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/get.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -77,7 +77,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/get.sharedseqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/get.sharedseqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -78,7 +78,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/hcluster.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/hcluster.xml Wed Sep 05 21:28:43 2012 -0500 @@ -76,7 +76,7 @@ <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/heatmap.bin.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/heatmap.bin.xml Wed Sep 05 21:28:43 2012 -0500 @@ -102,7 +102,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/heatmap.sim.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/heatmap.sim.xml Wed Sep 05 21:28:43 2012 -0500 @@ -86,7 +86,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/homova.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/homova.xml Wed Sep 05 21:28:43 2012 -0500 @@ -26,7 +26,7 @@ <data format="tabular" name="homova" label="${tool.name} on ${on_string}: homova"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/indicator.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/indicator.xml Wed Sep 05 21:28:43 2012 -0500 @@ -51,7 +51,7 @@ <data format="tabular" name="summary" label="${tool.name} on ${on_string}: indicator.summary"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/libshuff.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/libshuff.xml Wed Sep 05 21:28:43 2012 -0500 @@ -52,7 +52,7 @@ <data format="tabular" name="coverage" label="${tool.name} on ${on_string}: coverage"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/list.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/list.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -55,7 +55,7 @@ <data format="accnos" name="out_file" label="${tool.name} on ${on_string}: accnos" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/make.biom.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/make.biom.xml Wed Sep 05 21:28:43 2012 -0500 @@ -45,7 +45,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/make.design.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/make.design.xml Wed Sep 05 21:28:43 2012 -0500 @@ -29,7 +29,7 @@ <data format="design" name="design" label="${tool.name} on ${on_string}: design" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/make.fastq.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/make.fastq.xml Wed Sep 05 21:28:43 2012 -0500 @@ -24,7 +24,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/make.group.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/make.group.xml Wed Sep 05 21:28:43 2012 -0500 @@ -21,7 +21,7 @@ <data format="groups" name="output" label="${tool.name} on ${on_string}: group" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/make.shared.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/make.shared.xml Wed Sep 05 21:28:43 2012 -0500 @@ -48,7 +48,7 @@ <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/make.shared_from_biom.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/make.shared_from_biom.xml Wed Sep 05 21:28:43 2012 -0500 @@ -31,7 +31,7 @@ <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/mantel.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/mantel.xml Wed Sep 05 21:28:43 2012 -0500 @@ -27,7 +27,7 @@ <data format="tabular" name="mantel" label="${tool.name} on ${on_string}: mantel"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/merge.files.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/merge.files.xml Wed Sep 05 21:28:43 2012 -0500 @@ -54,7 +54,7 @@ <data format="input" name="output" label="${tool.name} on ${on_string}: ${merge.type}"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/merge.groups.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/merge.groups.xml Wed Sep 05 21:28:43 2012 -0500 @@ -85,7 +85,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/metastats.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/metastats.xml Wed Sep 05 21:28:43 2012 -0500 @@ -55,7 +55,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/nmds.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/nmds.xml Wed Sep 05 21:28:43 2012 -0500 @@ -41,7 +41,7 @@ <data format="tabular" name="stress_nmds" label="${tool.name} on ${on_string}: nmds.stress"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/normalize.shared.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/normalize.shared.xml Wed Sep 05 21:28:43 2012 -0500 @@ -50,7 +50,7 @@ <data format="shared" name="shared" label="${tool.name} on ${on_string}: norm.shared" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/otu.association.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/otu.association.xml Wed Sep 05 21:28:43 2012 -0500 @@ -44,7 +44,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/otu.hierarchy.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/otu.hierarchy.xml Wed Sep 05 21:28:43 2012 -0500 @@ -33,7 +33,7 @@ <data format="tabular" name="hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pairwise.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/pairwise.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -74,7 +74,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/parse.list.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/parse.list.xml Wed Sep 05 21:28:43 2012 -0500 @@ -27,7 +27,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/parsimony.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/parsimony.xml Wed Sep 05 21:28:43 2012 -0500 @@ -47,7 +47,7 @@ --> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pca.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/pca.xml Wed Sep 05 21:28:43 2012 -0500 @@ -40,7 +40,7 @@ <data format="txt" name="pca_loadings" label="${tool.name} on ${on_string}: pca.loadings" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pcoa.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/pcoa.xml Wed Sep 05 21:28:43 2012 -0500 @@ -18,7 +18,7 @@ <data format="tabular" name="loadings" label="${tool.name} on ${on_string}: loadings" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pcr.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/pcr.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -99,7 +99,7 @@ </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/phylo.diversity.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/phylo.diversity.xml Wed Sep 05 21:28:43 2012 -0500 @@ -74,7 +74,7 @@ --> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/phylotype.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/phylotype.xml Wed Sep 05 21:28:43 2012 -0500 @@ -41,7 +41,7 @@ <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/pre.cluster.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/pre.cluster.xml Wed Sep 05 21:28:43 2012 -0500 @@ -36,7 +36,7 @@ <data format="tabular" name="map_out" label="${tool.name} on ${on_string}: precluster.map" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/rarefaction.shared.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/rarefaction.shared.xml Wed Sep 05 21:28:43 2012 -0500 @@ -46,7 +46,7 @@ <data format="tabular" name="rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/rarefaction.single.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/rarefaction.single.xml Wed Sep 05 21:28:43 2012 -0500 @@ -69,7 +69,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/read.otu.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/read.otu.xml Wed Sep 05 21:28:43 2012 -0500 @@ -1,54 +0,0 @@ -<tool id="mothur_read_otu" name="Read.otu" version="1.16.0" force_history_refresh="True"> - <description>Read OTU list and group to create a shared file</description> - <command interpreter="python"> - mothur_wrapper.py - --cmd='read.otu' - --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared:'$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 ${on_string}: shared" /> - </outputs> - <requirements> - <requirement type="binary">mothur</requirement> - </requirements> - <tests> - </tests> - <help> -**Mothur Overview** - -Mothur_, initiated by Dr. Patrick Schloss and his software development team -in the Department of Microbiology and Immunology at The University of Michigan, -provides bioinformatics for the microbial ecology community. - -.. _Mothur: http://www.mothur.org/wiki/Main_Page - -**Command Documenation** - -The read.otu_ command is called before most of the OTU based mothur commands. It is included here explicitly to allow the creatation of a shared file from OTU list and group files. - -.. _read.otu: http://www.mothur.org/wiki/Read.otu - - </help> -</tool>
--- a/mothur/tools/mothur/remove.groups.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/remove.groups.xml Wed Sep 05 21:28:43 2012 -0500 @@ -94,7 +94,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/remove.lineage.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/remove.lineage.xml Wed Sep 05 21:28:43 2012 -0500 @@ -73,7 +73,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/remove.otus.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/remove.otus.xml Wed Sep 05 21:28:43 2012 -0500 @@ -55,7 +55,7 @@ <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/remove.rare.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/remove.rare.xml Wed Sep 05 21:28:43 2012 -0500 @@ -91,7 +91,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/remove.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/remove.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -77,7 +77,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/reverse.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/reverse.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -15,7 +15,7 @@ <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: rc.fasta" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/screen.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/screen.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -101,7 +101,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/sens.spec.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/sens.spec.xml Wed Sep 05 21:28:43 2012 -0500 @@ -42,7 +42,7 @@ <data format="tabular" name="sensspec" label="${tool.name} on ${on_string}: sensspec" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/seq.error.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/seq.error.xml Wed Sep 05 21:28:43 2012 -0500 @@ -146,7 +146,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/sffinfo.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/sffinfo.xml Wed Sep 05 21:28:43 2012 -0500 @@ -53,7 +53,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/shhh.flows.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/shhh.flows.xml Wed Sep 05 21:28:43 2012 -0500 @@ -79,7 +79,7 @@ <data format_source="tabular" name="shhh_counts" label="${tool.name} on ${on_string}: shhh.counts"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/shhh.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/shhh.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -32,7 +32,7 @@ <data format_source="txt" name="shhh_map" label="${tool.name} on ${on_string}: shhh.map"/> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/sort.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/sort.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -69,7 +69,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/split.abund.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/split.abund.xml Wed Sep 05 21:28:43 2012 -0500 @@ -98,7 +98,7 @@ --> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/split.groups.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/split.groups.xml Wed Sep 05 21:28:43 2012 -0500 @@ -30,7 +30,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/sub.sample.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/sub.sample.xml Wed Sep 05 21:28:43 2012 -0500 @@ -179,7 +179,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.qual.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/summary.qual.xml Wed Sep 05 21:28:43 2012 -0500 @@ -20,7 +20,7 @@ <data format="summary" name="out_summary" label="${tool.name} on ${on_string}: summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/summary.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -20,7 +20,7 @@ <data format="summary" name="out_summary" label="${tool.name} on ${on_string}: summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.shared.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/summary.shared.xml Wed Sep 05 21:28:43 2012 -0500 @@ -83,7 +83,7 @@ <data format="tabular" name="summary" label="${tool.name} on ${on_string}: shared.summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.single.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/summary.single.xml Wed Sep 05 21:28:43 2012 -0500 @@ -81,7 +81,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/summary.tax.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/summary.tax.xml Wed Sep 05 21:28:43 2012 -0500 @@ -61,7 +61,7 @@ <data format="summary" name="tax_summary" label="${tool.name} on ${on_string}: summary" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/tree.shared.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/tree.shared.xml Wed Sep 05 21:28:43 2012 -0500 @@ -136,7 +136,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/trim.flows.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/trim.flows.xml Wed Sep 05 21:28:43 2012 -0500 @@ -115,7 +115,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/trim.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/trim.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -151,7 +151,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/unifrac.unweighted.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/unifrac.unweighted.xml Wed Sep 05 21:28:43 2012 -0500 @@ -110,7 +110,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/unifrac.weighted.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/unifrac.weighted.xml Wed Sep 05 21:28:43 2012 -0500 @@ -117,7 +117,7 @@ </data> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/unique.seqs.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/unique.seqs.xml Wed Sep 05 21:28:43 2012 -0500 @@ -20,7 +20,7 @@ <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>
--- a/mothur/tools/mothur/venn.xml Wed Sep 05 19:49:43 2012 -0500 +++ b/mothur/tools/mothur/venn.xml Wed Sep 05 21:28:43 2012 -0500 @@ -88,7 +88,7 @@ <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </outputs> <requirements> - <requirement type="binary">mothur</requirement> + <requirement type="package" version="1.24.1">mothur</requirement> </requirements> <tests> </tests>