| Previous changeset 3:312539ee12f4 (2017-09-07) Next changeset 5:2ebca9da5e42 (2017-09-07) |
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Commit message:
planemo upload |
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modified:
splice_trap.xml |
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| diff -r 312539ee12f4 -r cd336e593a92 splice_trap.xml --- a/splice_trap.xml Thu Sep 07 15:29:43 2017 -0400 +++ b/splice_trap.xml Thu Sep 07 16:53:12 2017 -0400 |
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| @@ -4,17 +4,35 @@ <requirements> <requirement type="package" version="1.2.1.1">bowtie</requirement> </requirements> - <command detect_errors="exit_code"><![CDATA[ - perl $__tool_directory__/SpliceTrap.pl -p 8 -l $__tool_directory__ -d hg38v3 -1 "$input1" -2 "$input2" -s "$read_size" "$output1" "$output2" - ]]></command> + <command detect_errors="exit_code" interpreter="perl"> + $__tool_directory__/SpliceTrap.pl -p 8 -l $__tool_directory__ -d hg38v3 -1 + #if $input_type_conditional.spliceTrap_input_type == "paired" + $input_type_conditional.input_1 -2 $input_type_conditional.input_2 + #else + $input_type_conditional.input.forward -2 $input_type_conditional.input.reverse + #end if + -s $read_size $output1 $output2 + </command> <inputs> - <param type="data" name="input1" format="fastq" /> - <param type="data" name="input2" format="fastq" /> - <param name='read_size' type='integer' value='50' label="Read size" /> + <conditional name="input_type_conditional"> + <param name="spliceTrap_input_type" type="select" label="Input Type" help="Select between paired and paired collection"> + <option value="paired" selected="true">Paired</option> + <option value="paired_collection">Paired Collection</option> + </param> + <when value="paired"> + <param format='fastq' name='input_1' type='data' label="FASTQ file, reverse reads" /> + <param format='fastq' name='input_2' type='data' label="FASTQ file, forward reads" /> + </when> + <when value="paired_collection"> + <param format="fastq" name='input' type="data_collection" collection_type="paired" label="Select a paired collection" help="Specify paired dataset collection containing paired reads"/> + </when> + </conditional> + + <param name='read_size' type='integer' value='50' label="Read size" /> </inputs> <outputs> - <data name="output1" format="txt" /> - <data name="output2" format="txt" /> + <data format="txt" name="output1" /> + <data format="txt" name="output2" /> </outputs> <tests> <test> @@ -24,7 +42,7 @@ <output name="output2" file="output2.txt"/> </test> </tests> - <help> + <help> **SpliceTrap** </help> <citations> @@ -33,3 +51,4 @@ </citation> </citations> </tool> + |