| Previous changeset 0:a5f56370e870 (2015-11-12) Next changeset 2:013275060443 (2016-11-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 |
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modified:
sickle.xml |
| b |
| diff -r a5f56370e870 -r 43e081d32f90 sickle.xml --- a/sickle.xml Thu Nov 12 07:05:48 2015 -0500 +++ b/sickle.xml Sun Dec 06 11:31:57 2015 -0500 |
| [ |
| @@ -47,6 +47,18 @@ #end if #end if + #if str($readtype.single_or_paired) == "pe_collection": + pe -f "${readtype.input_paired.forward}" -r "${readtype.input_paired.reverse}" -o "${output_paired_coll.forward}" -p "${output_paired_coll.reverse}" -s "$output_paired_coll_single" + + #if $readtype.input_paired.forward.ext in ("fastq", "fastqsanger"): + -t sanger + #else if $readtype.input_paired.forward.ext == "fastqillumina": + -t illumina + #else if $readtype.input_paired.forward.ext == "fastqsolexa": + -t solexa + #end if + #end if + #if str($qual_threshold) != "": -q $qual_threshold #end if @@ -70,6 +82,7 @@ <option value="se" selected="true">Single-end</option> <option value="pe_combo">Paired-end (one interleaved input file)</option> <option value="pe_sep">Paired-end (two separate input files)</option> + <option value="pe_collection">Paired-end (as collection)</option> </param> <when value="se"> @@ -85,6 +98,10 @@ <param format="fastq" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" /> <param format="fastq" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" /> </when> + + <when value="pe_collection"> + <param format="fastq" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" /> + </when> </conditional> <param name="qual_threshold" value="20" min="0" type="integer" optional="true" label="Quality threshold" help="Threshold for trimming based on average quality in a window (-q)" /> @@ -119,30 +136,53 @@ <data name="output_paired_single" format_source="input_paired1" label="Singletons from paired-end output of ${tool.name} on ${on_string}"> <filter>readtype['single_or_paired'] == 'pe_sep'</filter> </data> + + <collection name="output_paired_coll" type="paired" structured_like="input_paired" inherit_format="true" label="Paired-end output of ${tool.name} on ${on_string}"> + <filter>readtype['single_or_paired'] == 'pe_collection'</filter> + </collection> + + <data name="output_paired_coll_single" format_source="input_paired['forward']" label="Singletons from paired-end output of ${tool.name} on ${on_string}"> + <filter>readtype['single_or_paired'] == 'pe_collection'</filter> + </data> </outputs> <tests> <test> <param name="single_or_paired" value="pe_combo" /> - <param name="input_combo" value="test.fastq" /> + <param name="input_combo" ftype="fastqsanger" value="test.fastq" /> <param name="qual_threshold" value="34" /> - <output name="output_combo" file="output.c1.fastq" /> - <output name="output_combo_single" file="output.s.fastq" /> + <output name="output_combo" ftype="fastqsanger" file="output.c1.fastq" /> + <output name="output_combo_single" ftype="fastqsanger" file="output.s.fastq" /> </test> <test> <param name="single_or_paired" value="pe_combo" /> - <param name="input_combo" value="test.fastq" /> + <param name="input_combo" ftype="fastqsanger" value="test.fastq" /> <param name="qual_threshold" value="34" /> <param name="output_n" value="true" /> - <output name="output_combo" file="output.c2.fastq" /> + <output name="output_combo" ftype="fastqsanger" file="output.c2.fastq" /> </test> <test> <param name="single_or_paired" value="pe_sep" /> - <param name="input_paired1" value="test.f.fastq" /> - <param name="input_paired2" value="test.r.fastq" /> + <param name="input_paired1" ftype="fastqsanger" value="test.f.fastq" /> + <param name="input_paired2" ftype="fastqsanger" value="test.r.fastq" /> <param name="qual_threshold" value="34" /> - <output name="output_paired1" file="output.f.fastq" /> - <output name="output_paired2" file="output.r.fastq" /> - <output name="output_paired_single" file="output.s.fastq" /> + <output name="output_paired1" ftype="fastqsanger" file="output.f.fastq" /> + <output name="output_paired2" ftype="fastqsanger" file="output.r.fastq" /> + <output name="output_paired_single" ftype="fastqsanger" file="output.s.fastq" /> + </test> + <test> + <param name="single_or_paired" value="pe_collection" /> + <param name="input_paired"> + <collection type="paired"> + <element name="forward" ftype="fastqsanger" value="test.f.fastq" /> + <element name="reverse" ftype="fastqsanger" value="test.r.fastq" /> + </collection> + </param> + <param name="qual_threshold" value="34" /> + <output_collection name="output_paired_coll" type="paired"> + <element name="forward" ftype="fastqsanger" file="output.f.fastq" /> + <element name="reverse" ftype="fastqsanger" file="output.r.fastq" /> + </output_collection> + <output name="output_paired_coll_single" ftype="fastqsanger" file="output.s.fastq" /> </test> </tests> <help> |