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comparison bamtools.xml @ 4:4d343c1f606b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
author iuc
date Wed, 04 Dec 2019 07:44:35 -0500
parents 04866f817daa
children befc9dad4ca8
comparison
equal deleted inserted replaced
3:04866f817daa 4:4d343c1f606b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bamtools" name="Convert, Merge, Randomize" version="2.4.0"> 2 <tool id="bamtools" name="Convert, Merge, Randomize" version="@VERSION@.0">
3 <description>BAM datasets and perform other transformations</description> 3 <description>BAM datasets and perform other transformations</description>
4 <requirements> 4 <macros>
5 <requirement type="package" version="2.4.0">bamtools</requirement> 5 <import>macros.xml</import>
6 <requirement type="package" version="1.3.1">samtools</requirement> 6 </macros>
7 </requirements> 7 <expand macro="requirements" />
8 <stdio> 8 <command detect_errors="exit_code">
9 <exit_code range="1:" />
10 </stdio>
11 <command>
12 <![CDATA[ 9 <![CDATA[
13 ##set up input files 10 ##set up input files
14 #for $bam_count, $input_bam in enumerate( $input_bams ): 11 ln -s '${input_bams}' localbam.bam &&
15 ln -s "${input_bam}" "localbam_${bam_count}.bam" && 12 ln -s '${input_bams.metadata.bam_index}' localbam.bam.bai &&
16 ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && 13 #if str( $analysis_type.analysis_type_selector ) == 'convert':
17 #end for 14 #if str( $analysis_type.format_type.format_type_selector ) == 'pileup':
18 #if str( $analysis_type.analysis_type_selector ) == "convert": 15 #set $reference_fasta_filename = 'localref.fa'
19 #if str( $analysis_type.format_type.format_type_selector ) == "pileup": 16 #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == 'history':
20 #set $reference_fasta_filename = "localref.fa" 17 ln -s '${analysis_type.format_type.reference_source.ref_file}' '${reference_fasta_filename}' &&
21 #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history": 18 samtools faidx '${reference_fasta_filename}' 2>&1 || echo 'Error running samtools faidx for bamtools convert' >&2 &&
22 ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &&
23 samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for bamtools convert" >&2 &&
24 #else: 19 #else:
25 #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path ) 20 #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )
26 #end if 21 #end if
27 #end if 22 #end if
28 #end if 23 #end if
29 bamtools 24 bamtools
30 #if str( $analysis_type.analysis_type_selector ) == "convert": 25 #if str( $analysis_type.analysis_type_selector ) == 'convert':
31 convert 26 convert
32 -format ${analysis_type.format_type.format_type_selector} 27 -format ${analysis_type.format_type.format_type_selector}
33 #if str( $analysis_type.format_type.format_type_selector ) == "pileup": 28 #if str( $analysis_type.format_type.format_type_selector ) == 'pileup':
34 ${analysis_type.format_type.mapqual} 29 ${analysis_type.format_type.mapqual}
35 -fasta "${reference_fasta_filename}" 30 -fasta '${reference_fasta_filename}'
36 #elif str( $analysis_type.format_type.format_type_selector ) == "sam": 31 #elif str( $analysis_type.format_type.format_type_selector ) == 'sam':
37 ${analysis_type.format_type.noheader} 32 ${analysis_type.format_type.noheader}
38 #end if 33 #end if
39 -out $out_file1 34 -out '$out_file1'
40 #elif str( $analysis_type.analysis_type_selector ) == "count": 35 #elif str( $analysis_type.analysis_type_selector ) == 'count':
41 count 36 count
42 > $out_file1 37 > '$out_file1'
43 #elif str( $analysis_type.analysis_type_selector ) == "coverage": 38 #elif str( $analysis_type.analysis_type_selector ) == 'coverage':
44 coverage 39 coverage
45 -out $out_file1 40 -out '$out_file1'
46 #elif str( $analysis_type.analysis_type_selector ) == "header": 41 #elif str( $analysis_type.analysis_type_selector ) == 'header':
47 header 42 header
48 > $out_file1 43 > '$out_file1'
49 #elif str( $analysis_type.analysis_type_selector ) == "merge": 44 #elif str( $analysis_type.analysis_type_selector ) == 'merge':
50 merge 45 merge
51 -out $out_file1 46 -out '$out_file1'
52 #elif str( $analysis_type.analysis_type_selector ) == "random": 47 #elif str( $analysis_type.analysis_type_selector ) == 'random':
53 random 48 random
54 -n ${analysis_type.count} 49 -n ${analysis_type.count}
55 -seed ${analysis_type.seed} 50 -seed ${analysis_type.seed}
56 -out $out_file1 51 -out '$out_file1'
57 #elif str( $analysis_type.analysis_type_selector ) == "revert": 52 #elif str( $analysis_type.analysis_type_selector ) == 'revert':
58 revert 53 revert
59 ${analysis_type.keepDuplicate} 54 ${analysis_type.keepDuplicate}
60 ${analysis_type.keepQualities} 55 ${analysis_type.keepQualities}
61 -out $out_file1 56 -out '$out_file1'
62 #elif str( $analysis_type.analysis_type_selector ) == "sort": 57 #elif str( $analysis_type.analysis_type_selector ) == 'sort':
63 sort 58 sort
64 ${analysis_type.byname} 59 ${analysis_type.byname}
65 -out $out_file1 60 -out '$out_file1'
66 #end if 61 #end if
67 #for $bam_count, $input_bam in enumerate( $input_bams ): 62 -in localbam.bam
68 -in "localbam_${bam_count}.bam"
69 #end for
70 ]]> 63 ]]>
71 </command> 64 </command>
72 <inputs> 65 <inputs>
73 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> 66 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" />
74 <conditional name="analysis_type"> 67 <conditional name="analysis_type">
75 <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool"> 68 <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">
76 <option value="convert">Convert</option> 69 <option value="convert">Convert</option>
77 <option value="count">Count</option> 70 <option value="count">Count</option>
78 <option value="coverage">Coverage</option> 71 <option value="coverage">Coverage</option>
151 <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" /> 144 <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" />
152 <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" /> 145 <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" />
153 <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" /> 146 <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" />
154 <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" /> 147 <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" />
155 <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" /> 148 <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" />
149 <when input="analysis_type.analysis_type_selector" value="count" format="tabular" />
156 <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" /> 150 <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" />
157 <when input="analysis_type.analysis_type_selector" value="merge" format="bam" /> 151 <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />
158 <when input="analysis_type.analysis_type_selector" value="random" format="bam" /> 152 <when input="analysis_type.analysis_type_selector" value="random" format="bam" />
159 <when input="analysis_type.analysis_type_selector" value="revert" format="bam" /> 153 <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />
160 <when input="analysis_type.analysis_type_selector" value="sort" format="bam" /> 154 <when input="analysis_type.analysis_type_selector" value="sort" format="bam" />
167 <param name="analysis_type_selector" value="convert"/> 161 <param name="analysis_type_selector" value="convert"/>
168 <param name="format_type_selector" value="pileup"/> 162 <param name="format_type_selector" value="pileup"/>
169 <param name="reference_source_selector" value="history" /> 163 <param name="reference_source_selector" value="history" />
170 <param name="mapqual" value="true" /> 164 <param name="mapqual" value="true" />
171 <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/> 165 <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>
172 <output name="output_bam" file="bamtools-convert-pileup.pu" /> 166 <output name="out_file1" file="bamtools-convert-pileup.pu" />
173 </test> 167 </test>
174 <test> 168 <test>
175 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> 169 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
176 <param name="analysis_type_selector" value="count"/> 170 <param name="analysis_type_selector" value="count"/>
177 <output name="output_bam" file="bamtools-count.tab" /> 171 <output name="out_file1" file="bamtools-count.tab" />
178 </test> 172 </test>
179 <test> 173 <test>
180 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> 174 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
181 <param name="analysis_type_selector" value="coverage"/> 175 <param name="analysis_type_selector" value="coverage"/>
182 <output name="output_bam" file="bamtools-coverage.tab" /> 176 <output name="out_file1" file="bamtools-coverage.tab" />
183 </test> 177 </test>
184 <test> 178 <test>
185 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> 179 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
186 <param name="analysis_type_selector" value="header"/> 180 <param name="analysis_type_selector" value="header"/>
187 <output name="output_bam" file="bamtools-header.txt" /> 181 <output name="out_file1" file="bamtools-header.txt" />
188 </test> 182 </test>
189 </tests> 183 </tests>
190 <help> 184 <help>
191 185
192 **What is does** 186 **What is does**