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comparison sRNAPipe.xml @ 60:9645d995fb3c draft

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Fix for spaces in datasets names.
author pierre.pouchin
date Wed, 24 Oct 2018 07:40:20 -0400
parents eeb89c3331ad
children 9185ca0a7b43
comparison
equal deleted inserted replaced
59:eeb89c3331ad 60:9645d995fb3c
1 <tool id="sRNAPipe" name="sRNAPipe" version="1.0"> 1 <tool id="sRNAPipe" name="sRNAPipe" version="1.0">
2 <description>In-depth study of small RNA</description> 2 <description>In-depth study of small RNA</description>
3 <command interpreter="perl"> 3 <command><![CDATA[
4 4 perl '$__tool_directory__/bin/sRNAPipe.pl'
5 ./bin/sRNAPipe.pl 5
6 6 --fastq '${first_input}'
7 --fastq ${first_input} 7 --fastq_n '${first_input.name}'
8 --fastq_n ${first_input.name}
9 #for $input_file in $input_files: 8 #for $input_file in $input_files:
10 --fastq ${input_file.additional_input} 9 --fastq '${input_file.additional_input}'
11 --fastq_n ${input_file.additional_input.name} 10 --fastq_n '${input_file.additional_input.name}'
12 #end for 11 #end for
13 12
14 #if $Genome.refGenomeSource == "history": 13 #if $Genome.refGenomeSource == "history":
15 --ref "${Genome.ownFile}" 14 --ref '${Genome.ownFile}'
16 --build_index 15 --build_index
17 #else: 16 #else:
18 --ref "${Genome.indices.fields.path}" 17 --ref '${Genome.indices.fields.path}'
19 #end if 18 #end if
20 19
21 #if $tRNAs.refGenomeSource == "history": 20 #if $tRNAs.refGenomeSource == "history":
22 --tRNAs "${tRNAs.ownFile}" 21 --tRNAs '${tRNAs.ownFile}'
23 --build_tRNAs 22 --build_tRNAs
24 #elif $tRNAs.refGenomeSource == "none": 23 #elif $tRNAs.refGenomeSource == "none":
25 --tRNAs "None" 24 --tRNAs "None"
26 #else: 25 #else:
27 --tRNAs "${tRNAs.indices.fields.path}" 26 --tRNAs '${tRNAs.indices.fields.path}'
28 #end if 27 #end if
29 28
30 #if $snRNAs.refGenomeSource == "history": 29 #if $snRNAs.refGenomeSource == "history":
31 --snRNAs "${snRNAs.ownFile}" 30 --snRNAs '${snRNAs.ownFile}'
32 --build_snRNAs 31 --build_snRNAs
33 #elif $snRNAs.refGenomeSource == "none": 32 #elif $snRNAs.refGenomeSource == "none":
34 --snRNAs "None" 33 --snRNAs "None"
35 #else: 34 #else:
36 --snRNAs "${snRNAs.indices.fields.path}" 35 --snRNAs '${snRNAs.indices.fields.path}'
37 #end if 36 #end if
38 37
39 #if $rRNAs.refGenomeSource == "history": 38 #if $rRNAs.refGenomeSource == "history":
40 --rRNAs "${rRNAs.ownFile}" 39 --rRNAs "${rRNAs.ownFile}"
41 --build_rRNAs 40 --build_rRNAs
42 #elif $rRNAs.refGenomeSource == "none": 41 #elif $rRNAs.refGenomeSource == "none":
43 --rRNAs "None" 42 --rRNAs "None"
44 #else: 43 #else:
45 --rRNAs "${rRNAs.indices.fields.path}" 44 --rRNAs '${rRNAs.indices.fields.path}'
46 #end if 45 #end if
47 46
48 #if $miRNAs.refGenomeSource == "history": 47 #if $miRNAs.refGenomeSource == "history":
49 --miRNAs "${miRNAs.ownFile}" 48 --miRNAs '${miRNAs.ownFile}'
50 --build_miRNAs 49 --build_miRNAs
51 #else: 50 #else:
52 --miRNAs "${miRNAs.indices.fields.path}" 51 --miRNAs '${miRNAs.indices.fields.path}'
53 #end if 52 #end if
54 53
55 #if $transcripts.refGenomeSource == "history": 54 #if $transcripts.refGenomeSource == "history":
56 --transcripts "${transcripts.ownFile}" 55 --transcripts '${transcripts.ownFile}'
57 --build_transcripts 56 --build_transcripts
58 #else: 57 #else:
59 --transcripts "${transcripts.indices.fields.path}" 58 --transcripts '${transcripts.indices.fields.path}'
60 #end if 59 #end if
61 60
62 #if $TE.refGenomeSource == "history": 61 #if $TE.refGenomeSource == "history":
63 --TE "${TE.ownFile}" 62 --TE '${TE.ownFile}'
64 --build_TE 63 --build_TE
65 #else: 64 #else:
66 --TE "${TE.indices.fields.path}" 65 --TE '${TE.indices.fields.path}'
67 #end if 66 #end if
68 67
69 --si_min $si_min 68 --si_min $si_min
70 --si_max $si_max 69 --si_max $si_max
71 --pi_min $pi_min 70 --pi_min $pi_min
76 --mis $mis 75 --mis $mis
77 --misTE $misTE 76 --misTE $misTE
78 --dir $html_out.files_path 77 --dir $html_out.files_path
79 --html $html_out 78 --html $html_out
80 --PPPon $PPPon 79 --PPPon $PPPon
80 ]]>
81 </command> 81 </command>
82 82
83 <requirements> 83 <requirements>
84 <requirement type="package" version="0.7.12">bwa</requirement> 84 <requirement type="package" version="0.7.12">bwa</requirement>
85 <requirement type="package" version="2.24">bedtools</requirement> 85 <requirement type="package" version="2.24">bedtools</requirement>