Mercurial > repos > iuc > khmer_filter_abundance
diff filter-abund.xml @ 8:82001a0a540c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
| author | iuc |
|---|---|
| date | Wed, 18 Dec 2019 20:58:02 +0000 |
| parents | 809e910a59ae |
| children | 92cbc7c0cb06 |
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--- a/filter-abund.xml Fri Sep 07 10:52:13 2018 -0400 +++ b/filter-abund.xml Wed Dec 18 20:58:02 2019 +0000 @@ -1,4 +1,4 @@ -<tool id="khmer_filter_abundance" name="Filter reads" version="@WRAPPER_VERSION@.0"> +<tool id="khmer_filter_abundance" name="khmer: Filter reads" version="@WRAPPER_VERSION@@TOOL_VERSION@"> <description> by minimal k-mer abundance </description> @@ -10,40 +10,36 @@ <expand macro="stdio" /> <expand macro="version" /> <command><![CDATA[ -set -xu && -#for $num, $input in enumerate($inputs) - ln -s ${input} filter-abund-sequence-${num} && -#end for +set -u && +@LINK_SEQUENCES@ mkdir output && cd output && @BINARY@ --cutoff=${cutoff} ${variable_coverage} @THREADS@ ${input_countgraph_filename} -../filter-abund-sequence* +@USE_SEQUENCES@ ]]> </command> <inputs> <expand macro="input_sequences_filenames" /> - <param name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue="" + <param argument="--variable_coverage" name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue="" label="Variable coverage" - help="Only trim when a sequence has high enough coverage; median abundance > 20 (--variable_coverage)" /> - <param name="cutoff" type="integer" value="2" label="Cutoff" - help="Trim at k-mers below this abundance. (--cutoff)" /> + help="Only trim when a sequence has high enough coverage; median abundance > 20" /> + <param argument="--cutoff" name="cutoff" type="integer" value="2" label="Cutoff" + help="Trim at k-mers below this abundance" /> <expand macro="input_countgraph_filename" /> </inputs> <outputs> - <collection name="filter-abund-sequences" type="list"> - <discover_datasets pattern="__name__" directory="output" /> - </collection> + <expand macro="output_sequences" extension="abundfilt"/> </outputs> <tests> <test> <param name="inputs" value="test-abund-read-2.fa" /> <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" /> - <output_collection name="filter-abund-sequences" type="list"> - <element name="filter-abund-sequence-0.abundfilt"> + <output_collection name="sequences" type="list"> + <element name="test-abund-read-2.fa"> <assert_contents> <has_text text="GGTTGACGGGGCTCAGGG" /> </assert_contents> @@ -55,8 +51,8 @@ <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" /> <param name="cutoff" value="1" /> - <output_collection name="filter-abund-sequences" type="list"> - <element name="filter-abund-sequence-0.abundfilt"> + <output_collection name="sequences" type="list"> + <element name="test-abund-read-2.fa"> <assert_contents> <has_text text="GGTTGACGGGGCTCAGGG" /> </assert_contents>