Mercurial > repos > bebatut > metaphlan2
changeset 17:bee6cb51b96d draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit bf4b8a62e4414d68a917f5b72f3aedf34facaff2-dirty
| author | bebatut |
|---|---|
| date | Thu, 05 Nov 2015 10:31:59 -0500 |
| parents | 84dd21255542 |
| children | 1aaa528861e6 |
| files | metaphlan2.xml |
| diffstat | 1 files changed, 6 insertions(+), 5 deletions(-) [+] |
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--- a/metaphlan2.xml Thu Nov 05 10:22:17 2015 -0500 +++ b/metaphlan2.xml Thu Nov 05 10:31:59 2015 -0500 @@ -35,9 +35,10 @@ --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200 - $bowtie2_output - #if not $bowtie2_output + # if $bowtie2_output: --bowtie2out $bowtie2_output_file + # else: + --no_map #end if -t $analysis_type.analysis_type_select @@ -112,7 +113,7 @@ <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/> - <param name="bowtie2_output" type='boolean' checked="true" truevalue="" falsevalue='--no_map' label="Store the output of BowTie2?" help="" /> + <param name="bowtie2_output" type='boolean' checked="true" label="Store the output of BowTie2?" help="" /> <param name="sam_output" type='boolean' label="Output a sam file?" help="" /> <param name="biom_output" type='boolean' label="Output a biom file?" help="" /> </inputs> @@ -125,7 +126,7 @@ <data format="bowtie2" name="bowtie2_output_file" metadata="input_sequence_file" label="Bowtie2 output on ${on_string} (MetaPhlAn)"> - <filter>bowtie2_output != '--no_map' </filter> + <filter>bowtie2_output</filter> </data> <data format="sam" name="sam_output_file" @@ -152,7 +153,7 @@ <param name="ignore_bacteria" value="" /> <param name="ignore_archaea" value="" /> <param name="stat_q" value="0.1" /> - <param name="bowtie2_output" value='--no_map' /> + <param name="bowtie2_output" value='True' /> <param name="sam_output" value='False' /> <param name="biom_output" value='False' /> <output name="output_file" file="profiled_metagenome.txt"/>