Mercurial > repos > sanbi-uwc > mothur_test
diff tools/mothur/merge.groups.xml @ 0:ee4fee239fe7 draft default tip
planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
| author | sanbi-uwc |
|---|---|
| date | Fri, 03 Jun 2016 09:32:47 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mothur/merge.groups.xml Fri Jun 03 09:32:47 2016 -0400 @@ -0,0 +1,160 @@ +<tool profile="16.07" id="mothur_merge_groups" name="Merge.groups" version="@WRAPPER_VERSION@.0"> + <description>Merge groups in a shared file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="aggressive"><![CDATA[ + echo 'merge.groups( + #if $design.source == "hist": + design=$design_dataset + #else: + design=$generated_design + #end if + #if $otu: + ,shared=$otu + #end if + #if $group: + ,group=$group + #end if + #if $groups: + ,groups=${ str($groups).replace(",","-") } + #end if + #if $label: + ,label=${ str($label).replace(",","-") } + #end if + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur && + + ## move output files to correct destination + #if $otu: + prefix="$otu" && + mv \${prefix%.dat}*.merge.* "$merged_shared" && + #end if + #if $group: + prefix="$group" && + mv \${prefix%.dat}*.merge.* "$merged_group" && + #end if + mv mothur.*.logfile "$logfile" + ]]></command> + <configfiles> + <configfile name="generated_design"><![CDATA[ + #if $design.source == 'build': + #for $grouping in $design.groupings: + #set grp_str = $grouping.groups.__str__ + #if grp_str != None and len(grp_str) > 0: + #for $grp in grp_str.split(','): + $grp $grouping.name + #end for + #end if + #end for + #end if + ]]></configfile> + </configfiles> + <inputs> + <param name="otu" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared Dataset"/> + <param name="label" type="select" label="label - Pick OTU Labels to include" optional="true" multiple="true"> + <expand macro="labeloptions"/> + </param> + <param name="group" type="data" format="mothur.groups" optional="true" label="group - Group Dataset"/> + <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> + <options> + <filter type="data_meta" ref="otu" key="groups"/> + </options> + </param> + <conditional name="design"> + <param name="source" type="select" label="Grouping Design from" help=""> + <option value="hist">Your History</option> + <option value="build">Build a grouping design</option> + </param> + <when value="hist"> + <param name="design_dataset" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/> + </when> + <when value="build"> + <repeat name="groupings" title="Grouping"> + <param name="name" type="text" label="Name for a new combined grouping"/> + <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping"> + <options> + <filter type="data_meta" ref="otu" key="groups"/> + </options> + </param> + </repeat> + </when> + </conditional> + </inputs> + <outputs> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/> + <data name="merged_shared" format="mothur.shared" label="${tool.name} on ${on_string}: merge.shared"> + <filter>otu</filter> + </data> + <data name="merged_group" format="mothur.groups" label="${tool.name} on ${on_string}: merge.groups"> + <filter>group</filter> + </data> + </outputs> + <tests> + <test><!-- test with shared file --> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="source" value="hist"/> + <param name="design_dataset" value="toymothur.design2"/> + <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/> + <expand macro="logfile-test"/> + </test> + <test><!-- test with shared file and label and group select --> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="label" value="0.05,0.22,0.38"/> + <param name="groups" value="forest,pasture"/> + <param name="source" value="hist"/> + <param name="design_dataset" value="toymothur.design2"/> + <output name="merged_shared" md5="11818d535bf88938dc063afca3f95b23" ftype="mothur.shared"/> + <expand macro="logfile-test"/> + </test> + <test><!-- test with group file --> + <param name="group" value="amazon.groups" ftype="mothur.groups"/> + <param name="source" value="hist"/> + <param name="design_dataset" value="toymothur.design2"/> + <output name="merged_group" md5="023ebd0668522e9531da5b061e6e9137" ftype="mothur.groups"/> + <expand macro="logfile-test"/> + </test> + <test><!-- test with design creation --> + <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> + <param name="source" value="build"/> + <repeat name="groupings"> + <param name="name" value="tardis"/> + <param name="groups" value="forest"/> + </repeat> + <repeat name="groupings"> + <param name="name" value="dalek"/> + <param name="groups" value="pasture"/> + </repeat> + <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documenation** + +The merge.groups_ command reads a shared_ file and a design file and merges the groups in the shared file that are in the same grouping in the design file. + +A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. : + ======= ======= + duck bird + cow mammal + pig mammal + goose bird + cobra reptile + ======= ======= + +The Make_Design tool can construct a design file from a Mothur dataset that contains group names. + +.. _shared: http://www.mothur.org/wiki/Shared_file +.. _merge.groups: http://www.mothur.org/wiki/Merge.groups +]]> + </help> + <expand macro="citations"/> +</tool>