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comparison repenrich.xml @ 5:02a8941da83b draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
author artbio
date Sun, 18 Nov 2018 17:07:02 -0500
parents d1f7ab78f7b5
children 6f4143893463
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4:d1f7ab78f7b5 5:02a8941da83b
1 <tool id="repenrich" name="RepEnrich" version="1.5.0"> 1 <tool id="repenrich" name="RepEnrich" version="1.6.0">
2 <description>Repeat Element Profiling</description> 2 <description>Repeat Element Profiling</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.0">bowtie</requirement> 4 <requirement type="package" version="1.2.0">bowtie</requirement>
5 <requirement type="package" version="0.1.19">samtools</requirement> 5 <requirement type="package" version="0.1.19">samtools</requirement>
6 <requirement type="package" version="2.20.1">bedtools</requirement> 6 <requirement type="package" version="2.20.1">bedtools</requirement>
14 #set input_base = 'Sample' 14 #set input_base = 'Sample'
15 #set baseReference = 'Genome' 15 #set baseReference = 'Genome'
16 16
17 ## uncompress fastq.gz or fastqsanger.gz if needed 17 ## uncompress fastq.gz or fastqsanger.gz if needed
18 #if $seq_method.seq_method_list == "single-read": 18 #if $seq_method.seq_method_list == "single-read":
19 #if $input_fastq.is_of_type("fastq.gz", "fastqsanger.gz"): 19 #if $seq_method.input_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
20 gunzip < '$input_fastq' > '${input_base}.fastq' && 20 gunzip < '$seq_method.input_fastq' > '${input_base}.fastq' &&
21 #else: 21 #else:
22 ln -f -s '$input_fastq' '${input_base}.fastq' && 22 ln -f -s '$seq_method.input_fastq' '${input_base}.fastq' &&
23 #end if
24 #elif $seq_method.seq_method_list == 'paired_collection':
25 #if $seq_method.input_fastq.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
26 gunzip < '$seq_method.input_fastq.forward' > '${input_base}.fastq' &&
27 gunzip < '$seq_method.input_fastq.reverse' > '${input_base}_2.fastq' &&
28 #else:
29 ln -f -s '$seq_method.input_fastq.forward' '${input_base}.fastq' &&
30 ln -f -s '$seq_method.input_fastq.reverse' '${input_base}_2.fastq' &&
23 #end if 31 #end if
24 #else: 32 #else:
25 #if $input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"): 33 #if $seq_method.input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
26 gunzip < '$input_fastq' > '${input_base}.fastq' && 34 gunzip < '$seq_method.input_fastq' > '${input_base}.fastq' &&
27 gunzip < '$input2_fastq' > '${input_base}_2.fastq' && 35 gunzip < '$seq_method.input2_fastq' > '${input_base}_2.fastq' &&
28 #else: 36 #else:
29 ln -f -s '$input_fastq' '${input_base}.fastq' && 37 ln -f -s '$seq_method.input_fastq' '${input_base}.fastq' &&
30 ln -f -s '$input2_fastq' '${input_base}_2.fastq' && 38 ln -f -s '$seq_method.input2_fastq' '${input_base}_2.fastq' &&
31 #end if 39 #end if
32 #end if 40 #end if
33 41
34 ln -f -s '$genome' '${baseReference}.fa' && 42 ln -f -s '$genome' '${baseReference}.fa' &&
35 bowtie-build '$genome' ${baseReference} && 43 bowtie-build '$genome' ${baseReference} &&
65 <inputs> 73 <inputs>
66 <conditional name="seq_method"> 74 <conditional name="seq_method">
67 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select"> 75 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select">
68 <option selected="True" value="single-read">Single-read sequencing</option> 76 <option selected="True" value="single-read">Single-read sequencing</option>
69 <option value="paired-end">Paired-end sequencing</option> 77 <option value="paired-end">Paired-end sequencing</option>
78 <option value="paired_collection">Paired-end Dataset Collection</option>
70 </param> 79 </param>
71 <when value="single-read"> 80 <when value="single-read">
72 <param format="fastq,fastqsanger" label="Single-reads" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> 81 <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Single-reads" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
73 </when> 82 </when>
74 <when value="paired-end"> 83 <when value="paired-end">
75 <param format="fastq,fastqsanger" label="1st paired-end sequencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> 84 <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="1st paired-end sequencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
76 <param format="fastq,fastqsanger" label="2nd paired-end sequencing dataset" name="input2_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> 85 <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="2nd paired-end sequencing dataset" name="input2_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
86 </when>
87 <when value="paired_collection">
88 <param name="input_fastq" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" type="data_collection" collection_type="paired" label="Paired Collection" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
77 </when> 89 </when>
78 </conditional> 90 </conditional>
79 <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" /> 91 <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" />
80 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/> 92 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/>
81 </inputs> 93 </inputs>