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comparison bwameth.xml @ 3:a6ea26c1f225 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit cbf959a50b9424974905a5551ef7b3c50da4d92a
author iuc
date Tue, 11 Apr 2017 09:19:24 -0400
parents 2e4674c16615
children 95219305823a
comparison
equal deleted inserted replaced
2:2e4674c16615 3:a6ea26c1f225
1 <tool id="bwameth" name="bwameth" version="0.2.0.2"> 1 <tool id="bwameth" name="bwameth" version="0.2.0.3" profile="17.01">
2 <description>Fast and accurate aligner of BS-Seq reads.</description> 2 <description>Fast and accurate aligner of BS-Seq reads.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2">samtools</requirement> 4 <requirement type="package" version="1.2">samtools</requirement>
5 <requirement type="package" version="0.2.0">bwameth</requirement> 5 <requirement type="package" version="0.2.0">bwameth</requirement>
6 </requirements> 6 </requirements>
14 #set index="index_dir/genome.fa" 14 #set index="index_dir/genome.fa"
15 #else 15 #else
16 #set index=$referenceSource.index.fields.path 16 #set index=$referenceSource.index.fields.path
17 #end if 17 #end if
18 18
19 ## Link in the files with a name that's appropriate
20 #if str($single_or_paired.single_or_paired_opts) == 'paired':
21 #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):
22 #set read1 = "input_f.fastq.gz"
23 #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
24 #set read1 = "input_f.fastq.bz2"
25 #else:
26 #set read1 = "input_f.fastq"
27 #end if
28 ln -f -s '${single_or_paired.input_mate1}' ${read1} &&
29
30 #if $single_or_paired.input_mate2.is_of_type("fastq.gz", "fastqsanger.gz"):
31 #set read2 = "input_r.fastq.gz"
32 #else if $single_or_paired.input_mate2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
33 #set read2 = "input_r.fastq.bz2"
34 #else:
35 #set read2 = "input_r.fastq"
36 #end if
37 ln -f -s '${single_or_paired.input_mate2}' ${read2} &&
38 #else if str($single_or_paired.single_or_paired_opts) == 'paired_collection':
39 #if $single_or_paired.input_mate1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
40 #set read1 = "input_f.fastq.gz"
41 #else if $single_or_paired.input_mate1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
42 #set read1 = "input_f.fastq.bz2"
43 #else:
44 #set read1 = "input_f.fastq"
45 #end if
46 ln -s '${single_or_paired.input_mate1.forward}' ${read1} &&
47
48 #if $single_or_paired.input_mate1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
49 #set read2 = "input_r.fastq.gz"
50 #else if $single_or_paired.input_mate1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
51 #set read2 = "input_r.fastq.bz2"
52 #else:
53 #set read2 = "input_r.fastq"
54 #end if
55 ln -s '${single_or_paired.input_mate1.reverse}' ${read2} &&
56 #else:
57 #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):
58 #set read1 = "input_f.fastq.gz"
59 #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):
60 #set read1 = "input_f.fastq.bz2"
61 #else:
62 #set read1 = "input_f.fastq"
63 #end if
64 ln -f -s '${single_or_paired.input_singles}' ${read1} &&
65 #end if
66
67
19 bwameth.py 68 bwameth.py
20 -t "\${GALAXY_SLOTS:-4}" 69 -t "\${GALAXY_SLOTS:-4}"
21 --reference "${index}" 70 --reference "${index}"
22 71
23 #if str($readGroup).strip() != "": 72 #if str($readGroup).strip() != "":
24 --read-group "${readGroup}" 73 --read-group "${readGroup}"
25 #end if 74 #end if
26 75
27 #if $single_or_paired.single_or_paired_opts == 'single': 76 #if $single_or_paired.single_or_paired_opts == 'single':
28 $single_or_paired.input_singles 77 $read1
29 #elif $single_or_paired.single_or_paired_opts == 'paired':
30 $single_or_paired.input_mate1 $single_or_paired.input_mate2
31 #else: 78 #else:
32 $single_or_paired.input_mate1.forward $single_or_paired.input_mate1.reverse 79 $read1 $read2
33 #end if 80 #end if
34 | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam - 81 | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam -
35 ]]> 82 ]]>
36 </command> 83 </command>
37 <inputs> 84 <inputs>
58 <option value="single">Single-end</option> 105 <option value="single">Single-end</option>
59 <option value="paired">Paired-end</option> 106 <option value="paired">Paired-end</option>
60 <option value="paired_collection">Paired-end Dataset Collection</option> 107 <option value="paired_collection">Paired-end Dataset Collection</option>
61 </param> 108 </param>
62 <when value="single"> 109 <when value="single">
63 <param name="input_singles" type="data" format="fastqsanger" label="FASTQ" help="FASTQ file." /> 110 <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ" help="FASTQ file." />
64 </when> 111 </when>
65 <when value="paired"> 112 <when value="paired">
66 <param name="input_mate1" type="data" format="fastqsanger" label="First read in pair" help="FASTQ file." /> 113 <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="First read in pair" help="FASTQ file." />
67 <param name="input_mate2" type="data" format="fastqsanger" label="Second read in pair" help="FASTQ file." /> 114 <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Second read in pair" help="FASTQ file." />
68 </when> 115 </when>
69 <when value="paired_collection"> 116 <when value="paired_collection">
70 <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." /> 117 <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." />
71 </when> 118 </when>
72 </conditional> 119 </conditional>
73 <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'"> 120 <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'">
74 <sanitizer sanitize="False"/> 121 <sanitizer sanitize="False"/>
75 </param> 122 </param>
80 <tests> 127 <tests>
81 <test> 128 <test>
82 <param name="referenceSource" value="history" /> 129 <param name="referenceSource" value="history" />
83 <param name="reference" value="ref.fa.gz" /> 130 <param name="reference" value="ref.fa.gz" />
84 <param name="single_or_paired_opts" value="paired" /> 131 <param name="single_or_paired_opts" value="paired" />
85 <param name="input_mate1" value="t_R1.fastq.gz" /> 132 <param name="input_mate1" value="t_R1.fastq.gz"/>
86 <param name="input_mate2" value="t_R2.fastq.gz" /> 133 <param name="input_mate2" value="t_R2.fastq.gz"/>
87 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> 134 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
88 </test> 135 </test>
89 <test> 136 <test>
90 <param name="referenceSource" value="history" /> 137 <param name="referenceSource" value="history" />
91 <param name="reference" value="ref.fa.gz" /> 138 <param name="reference" value="ref.fa.gz" />
92 <param name="single_or_paired_opts" value="paired_collection" /> 139 <param name="single_or_paired_opts" value="paired_collection" />
93 <param name="input_mate1"> 140 <param name="input_mate1">
94 <collection type="paired"> 141 <collection type="paired">
95 <element name="forward" value="t_R1.fastq.gz" /> 142 <element name="forward" value="t_R1.fastq.gz"/>
96 <element name="reverse" value="t_R2.fastq.gz" /> 143 <element name="reverse" value="t_R2.fastq.gz"/>
97 </collection> 144 </collection>
98 </param> 145 </param>
99 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/> 146 <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
100 </test> 147 </test>
101 </tests> 148 </tests>