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comparison picard_FastqToSam.xml @ 9:5eaa8a968300 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
author devteam
date Fri, 09 Oct 2015 17:43:13 -0400
parents 3a3234d7a2e8
children 05087b27692a
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equal deleted inserted replaced
8:3a3234d7a2e8 9:5eaa8a968300
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 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <stdio>
8 <exit_code range="1:" level="fatal"/>
9 </stdio>
7 <command> 10 <command>
8 @java_options@ 11 @java_options@
9 12
10 java -jar \$JAVA_JAR_PATH/picard.jar 13 java -jar \$JAVA_JAR_PATH/picard.jar
11 FastqToSam 14 FastqToSam
81 <when value="pe"> 84 <when value="pe">
82 <param name="fastq" type="data" format="fastq" label="Input fastq file for the first read in paired end data" help="FASTQ"/> 85 <param name="fastq" type="data" format="fastq" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
83 <param name="fastq2" type="data" format="fastq" label="Input fastq file for the second read of paired end data" help="FASTQ2"/> 86 <param name="fastq2" type="data" format="fastq" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
84 </when> 87 </when>
85 <when value="pc"> 88 <when value="pc">
86 <param name="fastq" type="data_collection" collection_type="paired" 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"/> 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"/>
87 </when> 90 </when>
88 </conditional> 91 </conditional>
89 92
90 <param name="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT"> 93 <param name="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT">
91 <option value="Standard" selected="True">Sanger (+33)</option> 94 <option value="Standard" selected="True">Sanger (+33)</option>
92 <option value="Illumina">Illumina (+64)</option> 95 <option value="Illumina">Illumina (+64)</option>
93 <option value="Solexa">Solexa (+66)</option> 96 <option value="Solexa">Solexa (+66)</option>
94 </param> 97 </param>
95 98
96 <param name="read_group_name" type="text" size="20" value="A" label="Read group name" help="READ_GROUP_NAME"/> 99 <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/>
97 <param name="sample_name" type="text" size="20" value="sample-a" label="Sample name" help="SAMPLE_NAME"/> 100 <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
98 <param name="library_name" type="text" size="20" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/> 101 <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
99 <param name="platform_unit" type="text" size="20" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/> 102 <param name="platform_unit" type="text" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
100 <param name="platform" type="text" size="20" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/> 103 <param name="platform" type="text" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
101 <param name="sequencing_center" type="text" size="20" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/> 104 <param name="sequencing_center" type="text" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
102 105
103 <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"/> 106 <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"/>
104 <param name="comment" type="text" size="20" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/> 107 <param name="comment" type="text" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
105 <param name="description" type="text" size="20" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/> 108 <param name="description" type="text" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
106 <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/> 109 <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
107 <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"/> 110 <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"/>
108 <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"/> 111 <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"/>
109 <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"/> 112 <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"/>
110 <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"/> 113 <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"/>
140 <param name="fastq2" value="picard_FastqToSam_read2.fq" ftype="fastq" /> 143 <param name="fastq2" value="picard_FastqToSam_read2.fq" ftype="fastq" />
141 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="bam" lines_diff="4"/> 144 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="bam" lines_diff="4"/>
142 </test> 145 </test>
143 </tests> 146 </tests>
144 147
145 <stdio>
146 <exit_code range="1:" level="fatal"/>
147 </stdio>
148
149 <help> 148 <help>
150 149
151 .. class:: infomark 150 .. class:: infomark
152 151
153 **Purpose** 152 **Purpose**
219 218
220 219
221 @more_info@ 220 @more_info@
222 221
223 </help> 222 </help>
223 <citations>
224 </citations>
224 </tool> 225 </tool>
225
226