Mercurial > repos > devteam > picard

annotate picard_FastqToSam.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
iuc
parents: 32
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1 <tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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2 <description>convert Fastq data into unaligned BAM</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 <token name="@WRAPPER_VERSION@">0</token>
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6 </macros>
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7 <xrefs>
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8 <xref type="bio.tools">picard_fastqtosam</xref>
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9 </xrefs>
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10 <expand macro="requirements"/>
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11 <command detect_errors="exit_code"><![CDATA[
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12 @java_options@
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13 #if str( $input_type.input_type_selector ) == "se":
1aac2a13842a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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14 #set fwd = $input_type.fastq
1aac2a13842a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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15 #set rev = None
1aac2a13842a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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16 #elif str( $input_type.input_type_selector ) == "pe":
1aac2a13842a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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17 #set fwd = $input_type.fastq
1aac2a13842a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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18 #set rev = $input_type.fastq2
1aac2a13842a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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19 #else
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20 #set fwq = $input_type.fastq.forward
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21 #set rev = $input_type.fastq.reverse
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22 #end if
1aac2a13842a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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23
1aac2a13842a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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24 #if $fwd.ext.endswith(".gz")
1aac2a13842a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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25 gunzip -c '$fwd' > fwd.fastq &&
1aac2a13842a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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26 #else
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27 ln -sf '$fwd' fwd.fastq &&
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28 #end if
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29 #if rev
1aac2a13842a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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30 #if rev.ext.endswith(".gz")
1aac2a13842a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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31 gunzip -c '$rev' > rev.fastq &&
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32 #else
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3f254c5ced1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
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33 ln -sf '$rev' rev.fastq &&
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34 #end if
1aac2a13842a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
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35 #end if
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36
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37 picard FastqToSam
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38
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39 --FASTQ fwd.fastq
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40 #if rev
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41 --FASTQ2 rev.fastq
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42 #end if
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43
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44 #if $fwd.ext.startswith("fastqillumina")
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45 --QUALITY_FORMAT "Illumina"
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46 #else if $fwd.ext.startswith("fastqsolexa")
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47 --QUALITY_FORMAT "Solexa"
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48 #else
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49 --QUALITY_FORMAT "Standard"
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50 #end if
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51 --OUTPUT '${outFile}'
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52 --READ_GROUP_NAME '${read_group_name}'
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53 --SAMPLE_NAME '${sample_name}'
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54
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55 #if str( $library_name ):
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56 --LIBRARY_NAME '${library_name}'
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57 #end if
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58
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59 #if str( $platform_unit ):
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60 --PLATFORM_UNIT '${platform_unit}'
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61 #end if
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62
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63 #if str( $platform ):
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64 --PLATFORM '${platform}'
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65 #end if
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66
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67 #if str( $sequencing_center ):
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68 --SEQUENCING_CENTER '${sequencing_center}'
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69 #end if
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70
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71 #if str( $predicted_insert_size ):
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72 --PREDICTED_INSERT_SIZE '${predicted_insert_size}'
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73 #end if
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74
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75 #if str( $comment ):
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76 --COMMENT '${comment}'
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77 #end if
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78
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79 #if str( $description ):
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80 --DESCRIPTION '${description}'
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81 #end if
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82
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83 #if str( $run_date ):
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84 --RUN_DATE '${run_date}'
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85 #end if
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86
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87 --MIN_Q '${min_q}'
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88 --MAX_Q '${max_q}'
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89 --STRIP_UNPAIRED_MATE_NUMBER '${strip_unpairied_mate_number}'
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90 --ALLOW_AND_IGNORE_EMPTY_LINES '${allow_and_ignore_empty_lines}'
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91
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92 --SORT_ORDER coordinate
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93 --VALIDATION_STRINGENCY '${validation_stringency}'
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94 --QUIET true
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95 --VERBOSITY ERROR
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96
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97 ]]></command>
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98 <inputs>
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99 <conditional name="input_type">
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100 <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types">
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101 <option value="se">Single end (single dataset)</option>
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102 <option value="pe">Paired end (two datasets)</option>
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103 <option value="pc">Paired collection</option>
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104 </param>
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105 <when value="se">
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106 <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for single end data" help="FASTQ"/>
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107 </when>
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108 <when value="pe">
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109 <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
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110 <param name="fastq2" type="data" format="fastq,fastq.gz" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
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111 </when>
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112 <when value="pc">
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113 <param name="fastq" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
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114 </when>
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115 </conditional>
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116 <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/>
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117 <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
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118 <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
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119 <param name="platform_unit" type="text" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
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120 <param name="platform" type="text" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
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121 <param name="sequencing_center" type="text" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
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122 <param name="predicted_insert_size" type="integer" min="0" max="100000" optional="True" label="Predicted median insert size, to insert into the read group header" help="PREDICTED_INSERT_SIZE; Optional"/>
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123 <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
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124 <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
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125 <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
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126 <param name="min_q" type="integer" value="0" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MIN_Q; An exception will be thrown if a quality is less than this value; default=0"/>
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127 <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/>
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128 <param name="strip_unpairied_mate_number" type="boolean" truevalue="true" falsevalue="false" label="If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name" help="STRIP_UNPAIRED_MATE_NUMBER; default=false"/>
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129 <param name="allow_and_ignore_empty_lines" type="boolean" truevalue="true" falsevalue="false" label="Allow (and ignore) empty lines" help="ALLOW_AND_IGNORE_EMPTY_LINES; default=false"/>
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130 <expand macro="VS"/>
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131 </inputs>
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132 <outputs>
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133 <data format="unsorted.bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
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134 </outputs>
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135 <tests>
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136 <test>
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137 <param name="input_type_selector" value="pe"/>
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138 <param name="read_group_name" value="A"/>
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139 <param name="sample_name" value="sample-a"/>
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140 <param name="library_name" value="A"/>
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141 <param name="platform_unit" value="A"/>
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142 <param name="platform" value="Illumina"/>
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143 <param name="sequencing_center" value="A"/>
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144 <param name="predicted_insert_size" value="300"/>
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145 <param name="comment" value="A"/>
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146 <param name="description" value="A"/>
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147 <param name="run_date" value="2014-10-10"/>
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148 <param name="min_q" value="0"/>
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149 <param name="max_q" value="93"/>
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150 <param name="strip_unpairied_mate_number" value="False"/>
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151 <param name="allow_and_ignore_empty_lines" value="False"/>
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152 <param name="validation_stringency" value="LENIENT"/>
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153 <param name="fastq" value="picard_FastqToSam_read1.fq.gz" ftype="fastq.gz"/>
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154 <param name="fastq2" value="picard_FastqToSam_read2.fq.gz" ftype="fastq.gz"/>
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155 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="unsorted.bam" lines_diff="4"/>
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156 </test>
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157 </tests>
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158 <help>
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159
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160 .. class:: infomark
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161
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162 **Purpose**
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163
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164 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
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165
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166 @dataset_collections@
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167
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168 @RG@
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169
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170 @description@
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171
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172 FASTQ=File
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173 F1=File Input fastq file for single end data, or first read in paired end
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174 data. Required.
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175
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176 FASTQ2=File
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177 F2=File Input fastq file for the second read of paired end data (if used).
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178
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179 QUALITY_FORMAT=FastqQualityFormat
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180 V=FastqQualityFormat A value describing how the quality values are encoded in the fastq. Either Solexa for
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181 pre-pipeline 1.3 style scores (solexa scaling + 66), Illumina for pipeline 1.3 and above
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182 (phred scaling + 64) or Standard for phred scaled scores with a character shift of 33.
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183 If this value is not specified, the quality format will be detected automatically.
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184 Default value: null. Possible values: {Solexa, Illumina, Standard}
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185
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186 READ_GROUP_NAME=String
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187 RG=String Read group name Default value: A.
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188
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189 SAMPLE_NAME=String
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190 SM=String Sample name to insert into the read group header Required.
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191
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192 LIBRARY_NAME=String
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193 LB=String The library name to place into the LB attribute in the read group header.
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194
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195 PLATFORM_UNIT=String
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196 PU=String The platform unit (often run_barcode.lane) to insert into the read group header.
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197
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198 PLATFORM=String
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199 PL=String The platform type (e.g. illumina, solid) to insert into the read group header.
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200
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201 SEQUENCING_CENTER=String
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202 CN=String The sequencing center from which the data originated.
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203
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204 PREDICTED_INSERT_SIZE=Integer
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205 PI=Integer Predicted median insert size, to insert into the read group header.
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206
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207 COMMENT=String
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208 CO=String Comment to include in the merged output file's header.
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209
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210 DESCRIPTION=String
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211 DS=String Inserted into the read group header.
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212
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213 RUN_DATE=Iso8601Date
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214 DT=Iso8601Date Date the run was produced, to insert into the read group header.
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215
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216 MIN_Q=Integer Minimum quality allowed in the input fastq. An exception will be thrown if a quality is
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217 less than this value. Default value: 0.
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218
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219 MAX_Q=Integer Maximum quality allowed in the input fastq. An exception will be thrown if a quality is
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220 greater than this value. Default value: 93.
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221
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222 STRIP_UNPAIRED_MATE_NUMBER=Boolean
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223 If true and this is an unpaired fastq any occurance of '/1' will be removed from the end
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224 of a read name. Default value: false. Possible values: {true, false}
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225
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226 ALLOW_AND_IGNORE_EMPTY_LINES=Boolean
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227 Allow (and ignore) empty lines Default value: false. Possible values: {true, false}
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228
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229
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230 @more_info@
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231
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232 </help>
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233 <expand macro="citations"/>
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234 </tool>