Mercurial > repos > sanbi-uwc > confil
changeset 1:d5b37a19547a draft
planemo upload for repository https://github.com/COMBAT-TB/confil commit 8239f5a11e0d9be3fb2b95e5c0241677da722bb9
author | sanbi-uwc |
---|---|
date | Wed, 13 Feb 2019 09:02:41 -0500 |
parents | 9963e812cd1d |
children | ca3c6f955c3e |
files | confil.xml test-data/seq.report test-data/seq.tab |
diffstat | 3 files changed, 58 insertions(+), 29 deletions(-) [+] |
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--- a/confil.xml Tue Feb 12 08:56:53 2019 -0500 +++ b/confil.xml Wed Feb 13 09:02:41 2019 -0500 @@ -3,24 +3,53 @@ <requirement type="package" version="7.0">click</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - confil --threads $threads --paired --cutoff $cutoff "$input1" "$input2" - ]]></command> + confil --threads $threads + #set $input_type = $input_type_conditional.input_type + #if $input_type == "paired_collection" + --paired + #end if + --cutoff $cutoff + #if $input_type == "single" + "${input_type_conditional.single_input}" + #elif $input_type == "paired_collection" + "${input_type_conditional.collection_input.forward}" "${input_type_conditional.collection_input.reverse}" + #end if + ]]> + </command> <inputs> - <param type="data" name="input1" format="fastq" /> - <param type="data" name="input2" format="fastq" /> - <param name="cutoff" type="integer" label="Cutoff percentage" - value="50" min="50" max="99" /> - <param name="threads" type="integer" label="Number of threads" - value="1" min="1" max="4" /> + <conditional name="input_type_conditional"> + <param name="input_type" type="select" label="Select Input Type"> + <option value="single" selected="true">Single Dataset</option> + <option value="paired_collection">Paired Collection</option> + </param> + <when value="single"> + <param name="single_input" type="data" format="fq,fastq,fastq.gz,fastqsanger" label="Select FASTQ Dataset" help="Specify dataset with single reads" /> + </when> + <when value="paired_collection"> + <param name="collection_input" format="fq,fastq,fastq.gz,fastqsanger" type="data_collection" collection_type="paired" label="Select Dataset Pair" help="Specify paired dataset collection containing paired reads" /> + </when> + </conditional> + <param name="cutoff" type="integer" label="Cutoff percentage" value="50" min="50" max="99" /> + <param name="threads" type="integer" label="Number of threads" value="1" min="1" max="4" /> </inputs> <outputs> - <data name="output1" format="tabular" from_work_dir="seq.report" /> + <data name="output" format="tabular" label="${tool.name} report" /> </outputs> <tests> <test> - <param name="input1" value="seq_1.fastq"/> - <param name="input2" value="seq_2.fastq"/> - <output name="output1" file="seq.report"/> + <param name="single_input" value="seq_1.fastq" /> + <param name="input_type" value="single" /> + <output name="output" ftype="tabular" file="seq.tab" /> + </test> + <test> + <param name="collection_input"> + <collection type="paired"> + <element name="forward" value="seq_1.fastq" /> + <element name="reverse" value="seq_2.fastq" /> + </collection> + </param> + <param name="input_type" value="paired_collection" /> + <output name="output" ftype='tabular' file="seq.tab" /> </test> </tests> <help><![CDATA[ @@ -34,7 +63,7 @@ --paired The filenames provided have paired-end reads --help Show this message and exit. - ]]></help> + ]]> </help> <citations> <citation type="bibtex"> @misc{githubconfil,
--- a/test-data/seq.report Tue Feb 12 08:56:53 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ - 28.34 1198200 1198200 U 0 unclassified - 71.66 3030398 1705 R 1 root - 71.59 3027326 90 R1 131567 cellular organisms - 71.33 3016097 5832 D 2 Bacteria - 56.09 2371684 139 D1 1783272 Terrabacteria group - 55.96 2366280 32 P 201174 Actinobacteria - 55.96 2366229 970 C 1760 Actinobacteria - 55.90 2363912 491 O 85007 Corynebacteriales - 55.88 2363031 1244 F 1762 Mycobacteriaceae - 55.84 2361413 2074448 G 1763 Mycobacterium - 6.64 280596 161419 G1 77643 Mycobacterium tuberculosis complex - 2.50 105696 74351 S 1773 Mycobacterium tuberculosis - 0.16 6824 6824 S1 747369 Mycobacterium tuberculosis R1207 - 0.03 1383 827 S1 83332 Mycobacterium tuberculosis H37Rv - 0.01 266 266 S2 757419 Mycobacterium tuberculosis H37RvCO - \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seq.tab Wed Feb 13 09:02:41 2019 -0500 @@ -0,0 +1,16 @@ + 28.34 1198200 1198200 U 0 unclassified + 71.66 3030398 1705 R 1 root + 71.59 3027326 90 R1 131567 cellular organisms + 71.33 3016097 5832 D 2 Bacteria + 56.09 2371684 139 D1 1783272 Terrabacteria group + 55.96 2366280 32 P 201174 Actinobacteria + 55.96 2366229 970 C 1760 Actinobacteria + 55.90 2363912 491 O 85007 Corynebacteriales + 55.88 2363031 1244 F 1762 Mycobacteriaceae + 55.84 2361413 2074448 G 1763 Mycobacterium + 6.64 280596 161419 G1 77643 Mycobacterium tuberculosis complex + 2.50 105696 74351 S 1773 Mycobacterium tuberculosis + 0.16 6824 6824 S1 747369 Mycobacterium tuberculosis R1207 + 0.03 1383 827 S1 83332 Mycobacterium tuberculosis H37Rv + 0.01 266 266 S2 757419 Mycobacterium tuberculosis H37RvCO + \ No newline at end of file