Mercurial > repos > devteam > bamtools
comparison bamtools.xml @ 4:4d343c1f606b draft
"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 |
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| 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** |