Mercurial > repos > matthias > stacks2_clonefilter

comparison stacks_clonefilter.xml @ 6:b707e9def9ff draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
author matthias
date Thu, 20 Jun 2019 08:18:09 -0400
parents c4ed7dacee9b
children
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5:c4ed7dacee9b 6:b707e9def9ff
34 #end if 34 #end if
35 $retain_oligo 35 $retain_oligo
36 ## only supports fastq.gz output since the 36 ## only supports fastq.gz output since the
37 ## the program outputs empty files for fasta/fastq 37 ## the program outputs empty files for fasta/fastq
38 -y gzfastq 38 -y gzfastq
39 @TEE_APPEND_LOG@
40 @CAT_LOG_TO_STDERR@
39 41
40 ## move outputs such that Galaxy can find them 42 ## move outputs such that Galaxy can find them
41 #if $capture: 43 #if $capture:
42 #if $input_type.input_type_select == "single" 44 #if $input_type.input_type_select == "single"
43 && mv stacks_outputs/*.discards.fq.gz '$discarded' 45 && mv stacks_outputs/*.discards.fq.gz '$discarded'
57 <expand macro="fastq_input_bc"/> 59 <expand macro="fastq_input_bc"/>
58 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> 60 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
59 <param name="oligo_len_1" type="integer" value="0" label="Length of the single-end oligo sequence in dataset"/> 61 <param name="oligo_len_1" type="integer" value="0" label="Length of the single-end oligo sequence in dataset"/>
60 <param name="oligo_len_2" optional="true" type="integer" label="Length of the paired-end oligo sequence in dataset"/> 62 <param name="oligo_len_2" optional="true" type="integer" label="Length of the paired-end oligo sequence in dataset"/>
61 <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="Do not trim off the random oligo sequence (if oligo is inline)" /> 63 <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="Do not trim off the random oligo sequence (if oligo is inline)" />
64 <expand macro="in_log"/>
62 </inputs> 65 </inputs>
63 <outputs> 66 <outputs>
67 <expand macro="out_log"/>
64 <data format="fastqsanger.gz" name="clean" from_work_dir="outputs/R1.fq.gz" label="${tool.name} on ${on_string}"> 68 <data format="fastqsanger.gz" name="clean" from_work_dir="outputs/R1.fq.gz" label="${tool.name} on ${on_string}">
65 <filter>input_type['input_type_select'] == 'single'</filter> 69 <filter>input_type['input_type_select'] == 'single'</filter>
66 </data> 70 </data>
67 <collection name="clean_pair" type="paired" label="${tool.name} on ${on_string}"> 71 <collection name="clean_pair" type="paired" label="${tool.name} on ${on_string}">
68 <filter>input_type['input_type_select'] == 'paired'</filter> 72 <filter>input_type['input_type_select'] == 'paired'</filter>
80 <conditional name="input_type"> 84 <conditional name="input_type">
81 <param name="input_type_select" value="single" /> 85 <param name="input_type_select" value="single" />
82 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> 86 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
83 </conditional> 87 </conditional>
84 <param name="oligo_len_1" value="6" /> 88 <param name="oligo_len_1" value="6" />
89 <param name="add_log" value="yes" />
90 <output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/>
85 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> 91 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
86 </test> 92 </test>
87 <!-- single end, alt BCencoding, capture--> 93 <!-- single end, alt BCencoding, capture-->
88 <test> 94 <test>
89 <conditional name="input_type"> 95 <conditional name="input_type">