Mercurial > repos > iuc > mothur_heatmap_sim
diff heatmap.sim.xml @ 2:6c7e2e05f606 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
---|---|
date | Tue, 20 Mar 2018 22:14:21 -0400 |
parents | 002aec843953 |
children |
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--- a/heatmap.sim.xml Tue Sep 05 17:16:13 2017 -0400 +++ b/heatmap.sim.xml Tue Mar 20 22:14:21 2018 -0400 @@ -7,45 +7,45 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$count" count.dat && - #if $input.source == 'shared': - ln -s "$input.otu" input_otu.dat && - #else - ln -s "$input.dist" input_dist.dat && - #if $input.source == 'column': - ln -s "$input.name" input_name.dat && - #end if - #end if +## create symlinks to input datasets +ln -s '$count' count.dat && +#if $input.source == 'shared': + ln -s '$input.otu' input_otu.dat && +#else + ln -s '$input.dist' input_dist.dat && + #if $input.source == 'column': + ln -s '$input.name' input_name.dat && + #end if +#end if - echo 'heatmap.sim( - #if $input.source == "shared": - shared=input_otu.dat, - #if $input.label: - label=${ str($input.label).replace(",","-") }, - #end if - #if $input.groups: - groups=${ str($input.groups).replace(",","-") }, - #end if - #if $input.calc: - calc=${ str($input.calc).replace(",","-") }, - #end if - #elif $input.source == "column": - column=input_dist.dat, - name=input_name.dat, - #elif $input.source == "phylip": - phylip=input_dist.dat, - #end if - #if $count: - count=count.dat, - #end if - fontsize=$fontsize - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'heatmap.sim( + #if $input.source == "shared": + shared=input_otu.dat, + #if $input.label: + label=${ str($input.label).replace(",","-") }, + #end if + #if $input.groups: + groups=${ str($input.groups).replace(",","-") }, + #end if + #if $input.calc: + calc=${ str($input.calc).replace(",","-") }, + #end if + #elif $input.source == "column": + column=input_dist.dat, + name=input_name.dat, + #elif $input.source == "phylip": + phylip=input_dist.dat, + #end if + #if $count: + count=count.dat, + #end if + fontsize=$fontsize +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <conditional name="input"> @@ -87,6 +87,7 @@ </conditional> <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/> <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table" help="generated by count.seqs"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -109,14 +110,21 @@ <has_text text="U68640"/> </assert_contents> </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> <param name="source" value="shared"/> <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> <output_collection name="heatmaps" count="72"> - <element name="0.55.jest.heatmap" md5="c48bac26a84f657ead8dd43af0401317"/> + <element name="0.55.jest.heatmap"> + <assert_contents> + <has_text text="svg xmlns:svg="/> + <has_text text="Heatmap at distance 0.55"/> + </assert_contents> + </element> </output_collection> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> @@ -126,13 +134,18 @@ <param name="calc" value="jclass,jest,sorclass,sorest,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc"/> <param name="groups" value="forest,pasture"/> <output_collection name="heatmaps" count="30"> - <element name="0.03.braycurtis.heatmap" md5="6a3f261e1012edaf620f78b62eff5c88"/> + <element name="0.03.braycurtis.heatmap"> + <assert_contents> + <has_text text="svg xmlns:svg="/> + <has_text text="Heatmap at distance 0.03"/> + </assert_contents> + </element> </output_collection> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -147,7 +160,7 @@ .. _heatmap.sim: https://www.mothur.org/wiki/Heatmap.sim v.1.24.0: Updated to Mothur 1.33, added count parameter -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>