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comparison picard_FastqToSam.xml @ 25:3b55709c0a01 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 1ef1c65fa4d78e1332411af1999862d5a8f28125"
author iuc
date Sun, 20 Mar 2022 14:05:27 +0000
parents e65f2d5fd3d8
children c943f4a04af0
comparison
equal deleted inserted replaced
24:e65f2d5fd3d8 25:3b55709c0a01
1 <tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="20.01">
2 <description>convert Fastq data into unaligned BAM</description> 2 <description>convert Fastq data into unaligned BAM</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">1</token> 5 <token name="@WRAPPER_VERSION@">2</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">picard_fastqtosam</xref> 8 <xref type="bio.tools">picard_fastqtosam</xref>
9 </xrefs> 9 </xrefs>
10 <expand macro="requirements" /> 10 <expand macro="requirements" />
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 @java_options@ 12 @java_options@
13 #if str( $input_type.input_type_selector ) == "se":
14 #set fwd = $input_type.fastq
15 #set rev = None
16 #elif str( $input_type.input_type_selector ) == "pe":
17 #set fwd = $input_type.fastq
18 #set rev = $input_type.fastq2
19 #else
20 #set fwq = $input_type.fastq.forward
21 #set rev = $input_type.fastq.reverse
22 #end if
23
24 #if $fwd.ext.endswith(".gz")
25 gunzip -c '$fwd' > fwd.fastq &&
26 #else
27 ln -s '$fwd' fwd.fastq &&
28 #end if
29 #if rev
30 #if rev.ext.endswith(".gz")
31 gunzip -c '$rev' > rev.fastq &&
32 #else
33 ln -s '$rev' rev.fastq &&
34 #end if
35 #end if
36
13 picard 37 picard
14 FastqToSam 38 FastqToSam
15 39
16 #if str( $input_type.input_type_selector ) == "se": 40 FASTQ=fwd.fastq
17 FASTQ="${input_type.fastq}" 41 #if rev
18 #elif str( $input_type.input_type_selector ) == "pe": 42 FASTQ2=rev.fastq
19 FASTQ="${input_type.fastq}" 43 #end if
20 FASTQ2="${input_type.fastq2}" 44
21 #else 45 #if $fwd.ext.startswith("fastqillumina")
22 FASTQ="${input_type.fastq.forward}" 46 QUALITY_FORMAT="Illumina"
23 FASTQ2="${input_type.fastq.reverse}" 47 #else if $fwd.ext.startswith("fastqsolexa")
24 #end if 48 QUALITY_FORMAT="Solexa"
25 49 #else
26 QUALITY_FORMAT="${quality_format}" 50 QUALITY_FORMAT="Standard"
51 #end if
27 OUTPUT="${outFile}" 52 OUTPUT="${outFile}"
28 READ_GROUP_NAME="${read_group_name}" 53 READ_GROUP_NAME="${read_group_name}"
29 SAMPLE_NAME="${sample_name}" 54 SAMPLE_NAME="${sample_name}"
30 55
31 #if str( $library_name ): 56 #if str( $library_name ):
77 <option value="se">Single end (single dataset)</option> 102 <option value="se">Single end (single dataset)</option>
78 <option value="pe">Paired end (two datasets)</option> 103 <option value="pe">Paired end (two datasets)</option>
79 <option value="pc">Paired collection</option> 104 <option value="pc">Paired collection</option>
80 </param> 105 </param>
81 <when value="se"> 106 <when value="se">
82 <param name="fastq" type="data" format="fastq" label="Input fastq file for single end data" help="FASTQ"/> 107 <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for single end data" help="FASTQ"/>
83 </when> 108 </when>
84 <when value="pe"> 109 <when value="pe">
85 <param name="fastq" type="data" format="fastq" label="Input fastq file for the first read in paired end data" help="FASTQ"/> 110 <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
86 <param name="fastq2" type="data" format="fastq" label="Input fastq file for the second read of paired end data" help="FASTQ2"/> 111 <param name="fastq2" type="data" format="fastq,fastq.gz" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
87 </when> 112 </when>
88 <when value="pc"> 113 <when value="pc">
89 <param name="fastq" type="data_collection" collection_type="paired" format="fastq" 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"/> 114 <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"/>
90 </when> 115 </when>
91 </conditional> 116 </conditional>
92
93 <param name="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT">
94 <option value="Standard" selected="True">Sanger (+33)</option>
95 <option value="Illumina">Illumina (+64)</option>
96 <option value="Solexa">Solexa (+66)</option>
97 </param>
98 117
99 <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/> 118 <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/>
100 <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/> 119 <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
101 <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/> 120 <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
102 <param name="platform_unit" type="text" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/> 121 <param name="platform_unit" type="text" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
115 <expand macro="VS" /> 134 <expand macro="VS" />
116 135
117 </inputs> 136 </inputs>
118 137
119 <outputs> 138 <outputs>
120 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/> 139 <data format="unsorted.bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
121 </outputs> 140 </outputs>
122 141
123 <tests> 142 <tests>
124 <test> 143 <test>
125 <param name="input_type_selector" value="pe" /> 144 <param name="input_type_selector" value="pe" />
126 <param name="quality_format" value="Standard" />
127 <param name="read_group_name" value="A" /> 145 <param name="read_group_name" value="A" />
128 <param name="sample_name" value="sample-a" /> 146 <param name="sample_name" value="sample-a" />
129 <param name="library_name" value="A"/> 147 <param name="library_name" value="A"/>
130 <param name="platform_unit" value="A"/> 148 <param name="platform_unit" value="A"/>
131 <param name="platform" value="Illumina"/> 149 <param name="platform" value="Illumina"/>
137 <param name="min_q" value="0" /> 155 <param name="min_q" value="0" />
138 <param name="max_q" value="93" /> 156 <param name="max_q" value="93" />
139 <param name="strip_unpairied_mate_number" value="False" /> 157 <param name="strip_unpairied_mate_number" value="False" />
140 <param name="allow_and_ignore_empty_lines" value="False" /> 158 <param name="allow_and_ignore_empty_lines" value="False" />
141 <param name="validation_stringency" value="LENIENT"/> 159 <param name="validation_stringency" value="LENIENT"/>
142 <param name="fastq" value="picard_FastqToSam_read1.fq" ftype="fastq" /> 160 <param name="fastq" value="picard_FastqToSam_read1.fq.gz" ftype="fastq.gz" />
143 <param name="fastq2" value="picard_FastqToSam_read2.fq" ftype="fastq" /> 161 <param name="fastq2" value="picard_FastqToSam_read2.fq.gz" ftype="fastq.gz" />
144 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="bam" lines_diff="4"/> 162 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="unsorted.bam" lines_diff="4"/>
145 </test> 163 </test>
146 </tests> 164 </tests>
147 165
148 <help> 166 <help>
149 167