Mercurial > repos > jshay > filterinfo
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author | jshay |
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date | Tue, 20 Aug 2019 11:22:23 -0400 |
parents | e40ccd3eab44 |
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<tool id="filterinfo" name="Filter Info" version="0.1.1"> <description>Report proportion of reads in one file vs. the other</description> <requirements> </requirements> <command detect_errors="exit_code"><![CDATA[ '$__tool_directory__/filterinfo.sh' -1 #if str( $orig_cond.orig_type ) == "one_of_pair" '$orig_cond.orig' #else '$orig_cond.orig.forward' #end if -2 #if str( $filtered_cond.filtered_type ) == "one_of_pair" '$filtered_cond.filt' #else '$filtered_cond.filt.forward' #end if #if $ispaired '-p' #end if -o '$out' ]]></command> <inputs> <conditional name="orig_cond"> <param name="orig_type" type="select" label="Original Input Type"> <option value="one_of_pair">Fastq File</option> <option value="paired_collection">Paired Collection</option> </param> <when value="one_of_pair"> <param name="orig" type="data" format="fastqsanger" label="Fastq sequences before filtering" help="Specify a single fastq file (either unpaired or half of a pair)"/> </when> <when value="paired_collection"> <param name="orig" format="fastqsanger" type="data_collection" collection_type="paired" label="Fastq sequences before filtering" help="Specify paired dataset collection containing paired reads"/> </when> </conditional> <conditional name="filtered_cond"> <param name="filtered_type" type="select" label="Filtered Input Type"> <option value="one_of_pair">Fastq File</option> <option value="paired_collection">Paired Collection</option> </param> <when value="one_of_pair"> <param name="filt" type="data" format="fastqsanger" label="Fastq sequences after filtering" help="Specify a single fastq file (either unpaired or half of a pair)"/> </when> <when value="paired_collection"> <param name="filt" format="fastqsanger" type="data_collection" collection_type="paired" label="Fastq sequences before filtering" help="Specify paired dataset collection containing paired reads"/> </when> </conditional> <param name="ispaired" type="boolean" label="Do the input fastq files come from sets of paired reads?"/> </inputs> <outputs> <data name="out" format="tabular" /> </outputs> <tests> <test> <param name="orig_type" value="paired_collection"/> <param name="orig"> <collection type="paired"> <element name="forward" value="full.fq" /> <element name="reverse" value="full2.fq" /> </collection> </param> <param name="filtered_type" value="one_of_pair"/> <param name="filt" value="filtered.fq"/> <param name="ispaired" value="true"/> <output name="out" file="prop.tsv"/> </test> </tests> <help><![CDATA[ Usage: ./filterinfo.sh -1 full.fq -2 filtered.fq -o out.tsv ]]></help> <citations> <citation type="bibtex"> @misc{githubfilterinfo, author = {Shay, Julie}, year = {2019, title = {filterinfo}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/jashay90/galaxytools}, }</citation> </citations> </tool>