Mercurial > repos > devteam > bamtools
annotate bamtools.xml @ 2:ea3fc1adee75 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:33:26 -0500 |
| parents | 76b2f1eee508 |
| children | 04866f817daa |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
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ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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2 <tool id="bamtools" name="Convert, Merge, Randomize" version="0.0.2"> |
| 0 | 3 <description>BAM datasets and perform other transformations</description> |
| 4 <requirements> | |
| 5 <requirement type="package" version="2.3.0_2d7685d2ae">bamtools</requirement> | |
| 6 <requirement type="package" version="0.1.18">samtools</requirement> | |
| 7 </requirements> | |
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ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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8 |
| 0 | 9 <command> |
| 10 ##set up input files | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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11 |
| 0 | 12 #for $bam_count, $input_bam in enumerate( $input_bams ): |
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ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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13 ln -s "${input_bam}" "localbam_${bam_count}.bam" && |
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ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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14 ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" && |
| 0 | 15 #end for |
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ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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16 |
| 0 | 17 #if str( $analysis_type.analysis_type_selector ) == "convert": |
| 18 #if str( $analysis_type.format_type.format_type_selector ) == "pileup": | |
| 19 #set $reference_fasta_filename = "localref.fa" | |
| 20 #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history": | |
| 21 ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" && | |
| 22 samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for bamtools convert" >&2 && | |
| 23 #else: | |
| 24 #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path ) | |
| 25 #end if | |
| 26 #end if | |
| 27 #end if | |
| 28 | |
| 29 ##finished setting up inputs | |
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ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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30 |
| 0 | 31 ##start bamtools commandline |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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32 |
| 0 | 33 bamtools |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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34 |
| 0 | 35 #if str( $analysis_type.analysis_type_selector ) == "convert": |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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36 |
| 0 | 37 convert |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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38 |
| 0 | 39 -format ${analysis_type.format_type.format_type_selector} |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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40 |
| 0 | 41 #if str( $analysis_type.format_type.format_type_selector ) == "pileup": |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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42 |
| 0 | 43 ${analysis_type.format_type.mapqual} |
| 44 -fasta "${reference_fasta_filename}" | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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45 |
| 0 | 46 #elif str( $analysis_type.format_type.format_type_selector ) == "sam": |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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47 |
| 0 | 48 ${analysis_type.format_type.noheader} |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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49 |
| 0 | 50 #end if |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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51 |
| 0 | 52 -out $out_file1 |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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53 |
| 0 | 54 #elif str( $analysis_type.analysis_type_selector ) == "count": |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
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55 |
| 0 | 56 count |
| 57 > $out_file1 | |
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ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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changeset
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58 |
| 0 | 59 #elif str( $analysis_type.analysis_type_selector ) == "coverage": |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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60 |
| 0 | 61 coverage |
| 62 -out $out_file1 | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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changeset
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63 |
| 0 | 64 #elif str( $analysis_type.analysis_type_selector ) == "header": |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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65 |
| 0 | 66 header |
| 67 > $out_file1 | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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68 |
| 0 | 69 #elif str( $analysis_type.analysis_type_selector ) == "merge": |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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70 |
| 0 | 71 merge |
| 72 -out $out_file1 | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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73 |
| 0 | 74 #elif str( $analysis_type.analysis_type_selector ) == "random": |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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75 |
| 0 | 76 random |
| 77 -n ${analysis_type.count} | |
| 78 -seed ${analysis_type.seed} | |
| 79 -out $out_file1 | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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80 |
| 0 | 81 #elif str( $analysis_type.analysis_type_selector ) == "revert": |
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ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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82 |
| 0 | 83 revert |
| 84 ${analysis_type.keepDuplicate} | |
| 85 ${analysis_type.keepQualities} | |
| 86 -out $out_file1 | |
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ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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87 |
| 0 | 88 #elif str( $analysis_type.analysis_type_selector ) == "sort": |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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89 |
| 0 | 90 sort |
| 91 ${analysis_type.byname} | |
| 92 -out $out_file1 | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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93 |
| 0 | 94 #end if |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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95 |
| 0 | 96 #for $bam_count, $input_bam in enumerate( $input_bams ): |
| 97 -in "localbam_${bam_count}.bam" | |
| 98 #end for | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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99 |
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ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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100 |
| 0 | 101 </command> |
| 102 <inputs> | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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103 |
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ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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104 <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/> |
| 0 | 105 |
| 106 <conditional name="analysis_type"> | |
| 107 <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool"> | |
| 108 <option value="convert">Convert</option> | |
| 109 <option value="count">Count</option> | |
| 110 <option value="coverage">Coverage</option> | |
| 111 <option value="header">Header</option> | |
| 112 <option value="merge">Merge</option> | |
| 113 <option value="random">Random</option> | |
| 114 <option value="revert">Revert</option> | |
| 115 <!-- The sort option below is commented out as BAM files in Galaxy are reference sorted by dafault. --> | |
| 116 <!-- Allowing users for sort files may break donstream functionality. --> | |
| 117 <!-- To enable sort option simply uncomment the line below: --> | |
| 118 <!-- <option value="sort">Sort</option> --> | |
| 119 </param> | |
| 120 <when value="convert"> | |
| 121 <conditional name="format_type"> | |
| 122 <param name="format_type_selector" type="select" help="Select what to convert your BAM to"> | |
| 123 <option value="bed">BED</option> | |
| 124 <option value="fasta">FASTA</option> | |
| 125 <option value="fastq">FASTQ</option> | |
| 126 <option value="json">JSON</option> | |
| 127 <option value="pileup">Pileup</option> | |
| 128 <option value="sam">SAM</option> | |
| 129 <option value="yaml">YAML</option> | |
| 130 </param> | |
| 131 <when value="pileup"> | |
| 132 <conditional name="reference_source"> | |
| 133 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> | |
| 134 <option value="cached">Locally cached</option> | |
| 135 <option value="history">History</option> | |
| 136 </param> | |
| 137 <when value="cached"> | |
| 138 <param name="ref_file" type="select" label="Using reference genome"> | |
| 139 <options from_data_table="sam_fa_indexes"> | |
| 140 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> | |
| 141 </options> | |
| 142 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 143 </param> | |
| 144 </when> | |
| 145 <when value="history"> <!-- FIX ME!!!! --> | |
| 146 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
| 147 </when> | |
| 148 </conditional> | |
| 149 <param name="mapqual" type="boolean" truevalue="-mapqual" falsevalue="" label="Print quality scores?" /> | |
| 150 </when> | |
| 151 <when value="sam"> | |
| 152 <param name="noheader" type="boolean" truevalue="-noheader" falsevalue="" label="Do not print header" /> | |
| 153 </when> | |
| 154 </conditional> | |
| 155 </when> | |
| 156 <when value="count"> | |
| 157 <!-- Nothing to be done with count -> just count alignments in the input bam(s) --> | |
| 158 </when> | |
| 159 <when value="coverage"> | |
| 160 <!-- Nothing to be done with count -> just count alignments in the input bam(s) --> | |
| 161 </when> | |
| 162 <when value="header"> | |
| 163 <!-- Nothing to be done with count -> just count alignments in the input bam(s) --> | |
| 164 </when> | |
| 165 <when value="merge"> | |
| 166 <!-- Nothing to be done with count -> just count alignments in the input bam(s) --> | |
| 167 </when> | |
| 168 <when value="random"> | |
| 169 <param name="count" type="integer" value="10000" label="Number of random alignments to grab" help="No duplicate checking is perfomed" /> | |
| 170 <param name="seed" type="integer" value="1024" label="Random number generator seed" help="Use the same seed for reproducible results" /> | |
| 171 </when> | |
| 172 <when value="revert"> | |
| 173 <param name="keepDuplicate" type="boolean" truevalue="-keepDuplicate" falsevalue="" label="Keep duplicates marked" help="Do not remove duplicate marks" /> | |
| 174 <param name="keepQualities" type="boolean" truevalue="-keepQualities" falsevalue="" label="Keep base qualities" help="Do not replace qualities with contect of OQ tag" /> | |
| 175 </when> | |
| 176 <when value="sort"> | |
| 177 <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/> | |
| 178 </when> | |
| 179 </conditional> | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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180 |
| 0 | 181 </inputs> |
| 182 <outputs> | |
| 183 <data format="txt" name="out_file1"> | |
| 184 <change_format> | |
| 185 <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" /> | |
| 186 <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" /> | |
| 187 <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" /> | |
| 188 <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" /> | |
| 189 <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" /> | |
| 190 <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" /> | |
| 191 <when input="analysis_type.analysis_type_selector" value="merge" format="bam" /> | |
| 192 <when input="analysis_type.analysis_type_selector" value="random" format="bam" /> | |
| 193 <when input="analysis_type.analysis_type_selector" value="revert" format="bam" /> | |
| 194 <when input="analysis_type.analysis_type_selector" value="sort" format="bam" /> | |
| 195 </change_format> | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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196 </data> |
| 0 | 197 </outputs> |
| 198 <tests> | |
| 199 <test> | |
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ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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200 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> |
| 0 | 201 <param name="analysis_type_selector" value="convert"/> |
| 202 <param name="format_type_selector" value="pileup"/> | |
| 203 <param name="reference_source_selector" value="history" /> | |
| 204 <param name="mapqual" value="true" /> | |
| 205 <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/> | |
| 206 <output name="output_bam" file="bamtools-convert-pileup.pu" /> | |
| 207 </test> | |
| 208 <test> | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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209 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> |
| 0 | 210 <param name="analysis_type_selector" value="count"/> |
| 211 <output name="output_bam" file="bamtools-count.tab" /> | |
| 212 </test> | |
| 213 <test> | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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214 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> |
| 0 | 215 <param name="analysis_type_selector" value="coverage"/> |
| 216 <output name="output_bam" file="bamtools-coverage.tab" /> | |
| 217 </test> | |
| 218 <test> | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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219 <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/> |
| 0 | 220 <param name="analysis_type_selector" value="header"/> |
| 221 <output name="output_bam" file="bamtools-header.txt" /> | |
| 222 </test> | |
| 223 </tests> | |
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2
ea3fc1adee75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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224 |
| 0 | 225 <stdio> |
| 226 <exit_code range="1:" /> | |
| 227 </stdio> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/bamtools/bamtools commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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| 0 | 229 <help> |
| 230 | |
| 231 **What is does** | |
| 232 | |
| 233 BAMTools is a collection of utilities for manipulation on BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools). | |
| 234 This Galaxy implementation of BAMTools utilities includes seven utilities - Convert, Count, Coverage, Header, Merge, Random, and Revert - decsribed in detail below. | |
| 235 | |
| 236 ----- | |
| 237 | |
| 238 **Convert** | |
| 239 | |
| 240 Converts BAM dataset(s) into BED, FASTA, FASTQ, JSON, Pileup, SAM, or YAML formats. Note that the conversion to the pileup format requires providing a reference sequence either | |
| 241 cashed at this Galaxy instance, or provided by you as a FASTA dataset from History. | |
| 242 | |
| 243 ----- | |
| 244 | |
| 245 **Count** | |
| 246 | |
| 247 Counts a number of alignments in a BAM dataset(s). | |
| 248 | |
| 249 ----- | |
| 250 | |
| 251 **Coverage** | |
| 252 | |
| 253 Prints per-base coverage for a BAM dataset. | |
| 254 | |
| 255 ----- | |
| 256 | |
| 257 **Header** | |
| 258 | |
| 259 Prints header from a BAM dataset(s). | |
| 260 | |
| 261 ------ | |
| 262 | |
| 263 **Merge** | |
| 264 | |
| 265 Merges multiple BAM datasets into a single one. Obviously, you need to select multiple BAMs as input, which is done by pressing the "**Add new BAM dataset(s) to filter**" button. | |
| 266 | |
| 267 ------ | |
| 268 | |
| 269 **Random** | |
| 270 | |
| 271 Grabs a specified number of random lines from BAM dataset(s). | |
| 272 | |
| 273 ------ | |
| 274 | |
| 275 **Revert** | |
| 276 | |
| 277 Removes duplicate marks and restores original (non-recalibrated) base qualities. | |
| 278 | |
| 279 ----- | |
| 280 | |
| 281 .. class:: infomark | |
| 282 | |
| 283 **More information** | |
| 284 | |
| 285 Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki | |
| 286 | |
| 287 </help> | |
| 288 <citations> | |
| 289 <citation type="doi">10.1093/bioinformatics/btr174</citation> | |
| 290 </citations> | |
| 291 </tool> |