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1 <tool id="gatk_print_reads" name="Print Reads" version="0.0.1">
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2 <description>from BAM files</description>
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3 <requirements>
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4 <requirement type="package" version="1.4">gatk</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 </requirements>
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7 <macros>
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8 <import>gatk_macros.xml</import>
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9 </macros>
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10 <command interpreter="python">gatk_wrapper.py
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11 --max_jvm_heap_fraction "1"
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12 --stdout "${output_log}"
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13 #for $i, $input_bam in enumerate( $reference_source.input_bams ):
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14 -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
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15 #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
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16 -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
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17 #end if
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18 #end for
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19 -p 'java
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20 -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar"
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21 -T "PrintReads"
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22 ##--num_threads 4 ##hard coded, for now
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23 --out "${output_bam}"
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24 -et "NO_ET" ##ET no phone home
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25 #if $reference_source.reference_source_selector != "history":
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26 -R "${reference_source.ref_file.fields.path}"
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27 #end if
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28 --number "${number}"
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29 #if $platform:
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30 --platform "${platform}"
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31 #end if
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32 #if $read_group:
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33 --readGroup "${read_group}"
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34 #end if
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35 #for $sample_file in $sample_file_repeat:
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36 --sample_file "${sample_file.input_sample_file}"
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37 #end for
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38 #for $sample_name in $sample_name_repeat:
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39 --sample_name "${sample_name.sample_name}"
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40 #end for
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41 '
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42
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43 #include source=$standard_gatk_options#
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44
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45 </command>
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46 <inputs>
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47 <conditional name="reference_source">
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48 <expand macro="reference_source_selector_param" />
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49 <when value="cached">
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50 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;">
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51 <param name="input_bam" type="data" format="bam" label="BAM file">
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52 <validator type="unspecified_build" />
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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 -->
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54 </param>
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55 </repeat>
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56 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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57 <options from_data_table="gatk_picard_indexes">
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58 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
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59 </options>
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60 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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61 </param>
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62 </when>
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63 <when value="history"> <!-- FIX ME!!!! -->
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64 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;">
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65 <param name="input_bam" type="data" format="bam" label="BAM file" >
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66 </param>
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67 </repeat>
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68 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
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69 </when>
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70 </conditional>
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71
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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;" />
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73 <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" help="-platform,--platform &lt;platform&gt;" />
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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;" />
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75 <repeat name="sample_file_repeat" title="File containing a list of samples to include" help="-sf,--sample_file &lt;sample_file&gt;">
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76 <param name="input_sample_file" type="data" format="text" label="Sample file" />
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77 </repeat>
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78 <repeat name="sample_name_repeat" title="Sample name to be included in the analysis" help="-sn,--sample_name &lt;sample_name&gt;">
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79 <param name="sample_name" type="text" label="Sample name" />
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80 </repeat>
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81
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82 <expand macro="gatk_param_type_conditional" />
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83
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84 </inputs>
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85 <outputs>
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86 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
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87 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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88 </outputs>
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89 <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" />
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90 <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" />
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91 <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" />
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92 <repeat name="sample_file_repeat" title="File containing a list of samples to include">
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93 <param name="input_sample_file" type="data" format="text" label="Sample file" />
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94 </repeat>
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95 <repeat name="sample_name_repeat" title="Sample name to be included in the analysis">
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96 <param name="sample_name" type="text" label="Sample name" />
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97 </repeat>
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98 <tests>
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99 <test>
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100 <param name="reference_source_selector" value="history" />
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101 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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102 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
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103 <param name="number" value="-1" />
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104 <param name="platform" value="" />
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105 <param name="read_group" value="" />
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106 <param name="sample_file_repeat" value="0" />
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107 <param name="sample_name_repeat" value="0" />
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108 <param name="gatk_param_type_selector" value="basic" />
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109 <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" compare="contains"/>
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110 <output name="output_log" file="gatk/gatk_print_reads/gatk_print_reads_out_1.log.contains" compare="contains" />
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111 </test>
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112 </tests>
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113 <help>
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114 **What it does**
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115
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116 PrintReads can dynamically merge the contents of multiple input BAM files, resulting in merged output sorted in coordinate order.
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117
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118 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>`_.
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119
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120 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>`_.
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121
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122 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_.
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123
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124 ------
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125
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126 **Inputs**
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127
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128 GenomeAnalysisTK: PrintReads accepts one or more BAM or SAM input files.
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129
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130
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131 **Outputs**
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132
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133 The output is in BAM format.
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134
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135
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136 Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats.
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137
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138 -------
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139
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140 **Settings**::
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141
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142 number int -1 Print the first n reads from the file, discarding the rest
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143 platform String NA Exclude all reads with this platform from the output
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144 readGroup String NA Exclude all reads with this read group from the output
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145 sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times
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146 sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times.
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147
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148 @CITATION_SECTION@
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149 </help>
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150 </tool>
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