Mercurial > repos > devteam > print_reads
annotate print_reads.xml @ 1:64d5adc286bb draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:46:26 -0400 |
| parents | 6fc6b56b342e |
| children |
| rev | line source |
|---|---|
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64d5adc286bb
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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1 <tool id="gatk_print_reads" name="Print Reads" version="0.0.2"> |
| 0 | 2 <description>from BAM files</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.4">gatk</requirement> | |
| 5 <requirement type="package" version="0.1.18">samtools</requirement> | |
| 6 </requirements> | |
| 7 <macros> | |
| 8 <import>gatk_macros.xml</import> | |
| 9 </macros> | |
| 10 <command interpreter="python">gatk_wrapper.py | |
| 11 --max_jvm_heap_fraction "1" | |
| 12 --stdout "${output_log}" | |
| 13 #for $i, $input_bam in enumerate( $reference_source.input_bams ): | |
| 14 -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}" | |
| 15 #if str( $input_bam.input_bam.metadata.bam_index ) != "None": | |
| 16 -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index | |
| 17 #end if | |
| 18 #end for | |
| 19 -p 'java | |
| 20 -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar" | |
| 21 -T "PrintReads" | |
| 22 ##--num_threads 4 ##hard coded, for now | |
| 23 --out "${output_bam}" | |
| 24 -et "NO_ET" ##ET no phone home | |
| 25 #if $reference_source.reference_source_selector != "history": | |
| 26 -R "${reference_source.ref_file.fields.path}" | |
| 27 #end if | |
| 28 --number "${number}" | |
| 29 #if $platform: | |
| 30 --platform "${platform}" | |
| 31 #end if | |
| 32 #if $read_group: | |
| 33 --readGroup "${read_group}" | |
| 34 #end if | |
| 35 #for $sample_file in $sample_file_repeat: | |
| 36 --sample_file "${sample_file.input_sample_file}" | |
| 37 #end for | |
| 38 #for $sample_name in $sample_name_repeat: | |
| 39 --sample_name "${sample_name.sample_name}" | |
| 40 #end for | |
| 41 ' | |
| 42 | |
| 43 #include source=$standard_gatk_options# | |
| 44 | |
| 45 </command> | |
| 46 <inputs> | |
| 47 <conditional name="reference_source"> | |
| 48 <expand macro="reference_source_selector_param" /> | |
| 49 <when value="cached"> | |
| 50 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> | |
| 51 <param name="input_bam" type="data" format="bam" label="BAM file"> | |
| 52 <validator type="unspecified_build" /> | |
| 53 <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> | |
| 54 </param> | |
| 55 </repeat> | |
| 56 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
| 57 <options from_data_table="gatk_picard_indexes"> | |
| 58 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> | |
| 59 </options> | |
| 60 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 61 </param> | |
| 62 </when> | |
| 63 <when value="history"> <!-- FIX ME!!!! --> | |
| 64 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> | |
| 65 <param name="input_bam" type="data" format="bam" label="BAM file" > | |
| 66 </param> | |
| 67 </repeat> | |
| 68 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | |
| 69 </when> | |
| 70 </conditional> | |
| 71 | |
| 72 <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" help="-n,--number &lt;number&gt;" /> | |
| 73 <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" help="-platform,--platform &lt;platform&gt;" /> | |
| 74 <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" help="-readGroup,--readGroup &lt;readGroup&gt;" /> | |
| 75 <repeat name="sample_file_repeat" title="File containing a list of samples to include" help="-sf,--sample_file &lt;sample_file&gt;"> | |
|
1
64d5adc286bb
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
76 <param name="input_sample_file" type="data" format="txt" label="Sample file" /> |
| 0 | 77 </repeat> |
| 78 <repeat name="sample_name_repeat" title="Sample name to be included in the analysis" help="-sn,--sample_name &lt;sample_name&gt;"> | |
| 79 <param name="sample_name" type="text" label="Sample name" /> | |
| 80 </repeat> | |
| 81 | |
| 82 <expand macro="gatk_param_type_conditional" /> | |
| 83 | |
| 84 </inputs> | |
| 85 <outputs> | |
| 86 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" /> | |
| 87 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
| 88 </outputs> | |
| 89 <tests> | |
| 90 <test> | |
| 91 <param name="reference_source_selector" value="history" /> | |
| 92 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
| 93 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /> | |
| 94 <param name="number" value="-1" /> | |
| 95 <param name="platform" value="" /> | |
| 96 <param name="read_group" value="" /> | |
| 97 <param name="sample_file_repeat" value="0" /> | |
| 98 <param name="sample_name_repeat" value="0" /> | |
| 99 <param name="gatk_param_type_selector" value="basic" /> | |
| 100 <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" compare="contains"/> | |
| 101 <output name="output_log" file="gatk/gatk_print_reads/gatk_print_reads_out_1.log.contains" compare="contains" /> | |
| 102 </test> | |
| 103 </tests> | |
| 104 <help> | |
| 105 **What it does** | |
| 106 | |
| 107 PrintReads can dynamically merge the contents of multiple input BAM files, resulting in merged output sorted in coordinate order. | |
| 108 | |
| 109 For more information on the GATK Print Reads Walker, see this `tool specific page <http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_gatk_walkers_PrintReadsWalker.html>`_. | |
| 110 | |
| 111 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_. | |
| 112 | |
| 113 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_. | |
| 114 | |
| 115 ------ | |
| 116 | |
| 117 **Inputs** | |
| 118 | |
| 119 GenomeAnalysisTK: PrintReads accepts one or more BAM or SAM input files. | |
| 120 | |
| 121 | |
| 122 **Outputs** | |
| 123 | |
| 124 The output is in BAM format. | |
| 125 | |
| 126 | |
| 127 Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats. | |
| 128 | |
| 129 ------- | |
| 130 | |
| 131 **Settings**:: | |
| 132 | |
| 133 number int -1 Print the first n reads from the file, discarding the rest | |
| 134 platform String NA Exclude all reads with this platform from the output | |
| 135 readGroup String NA Exclude all reads with this read group from the output | |
| 136 sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times | |
| 137 sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times. | |
| 138 | |
| 139 @CITATION_SECTION@ | |
| 140 </help> | |
| 141 </tool> |