Mercurial > repos > iuc > khmer_filter_below_abundance_cutoff
diff filter-below-abund.xml @ 0:67b597ec0baf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
author | iuc |
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date | Wed, 11 Nov 2015 09:46:57 -0500 |
parents | |
children | e0e33e40d7c4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter-below-abund.xml Wed Nov 11 09:46:57 2015 -0500 @@ -0,0 +1,51 @@ +<tool id="khmer_filter_below_abundance_cutoff" name="Filter k-mers" version="@WRAPPER_VERSION@.0"> + <description> + below abundance cutoff of 50 + </description> + <macros> + <token name="@BINARY@">filter-below-abund.py</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <command><![CDATA[ + #for $num, $input in enumerate($inputs) + ln -s ${input} sequence-${num} && + #end for + mkdir output && + cd output && + $__tool_directory__/@BINARY@ + ${input_countgraph_filename} + #for $num, $input in enumerate($inputs) + ../sequence-${num} + #end for + ]]> + </command> + <inputs> + <expand macro="input_sequences_filenames" /> + <expand macro="input_countgraph_filename" /> + </inputs> + <outputs> + <collection name="sequence_files" type="list"> + <discover_datasets pattern="__name__" directory="output" /> + </collection> + </outputs> + <tests> + <test> + <param name="inputs" value="test-abund-read-2.fa" /> + <param name="input_countgraph_filename" value="test-abund-read-2.large.oxlicg" ftype="oxlicg" /> + <output_collection name="sequence_files"> + <element name="sequence-0.below" file="test-abund-read-2.fa.below" /> + </output_collection> + </test> + </tests> + <help><![CDATA[ +Trims fastq/fasta sequences at k-mers with abundance below 50 based on a provided k-mer countgraph. + +@HELP_FOOTER@ +]]></help> + <citations> + <expand macro="software-citation" /> + <expand macro="counting-citation" /> + </citations> +</tool>