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comparison picard_MeanQualityByCycle.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
comparison
equal deleted inserted replaced
32:f9242e01365a 33:3f254c5ced1d
1 <tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
2 <description>chart distribution of base qualities</description> 2 <description>chart distribution of base qualities</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@">0</token>
6 </macros> 6 </macros>
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="3.4.1">r-base</requirement>
9 </expand> 8 </expand>
10 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
11 @java_options@ 10 @java_options@
12 ##set up input files 11 ##set up input files
13 @symlink_element_identifier@ 12 @symlink_element_identifier@
14 #set $reference_fasta_filename = "localref.fa" 13 #set $reference_fasta_filename = "localref.fa"
15 14
16 @handle_reference_source@ 15 @handle_reference_source@
17 16
18 picard 17 picard MeanQualityByCycle
19 MeanQualityByCycle 18 --INPUT '$escaped_element_identifier'
20 INPUT='$escaped_element_identifier' 19 --OUTPUT '${outFile}'
21 OUTPUT="${outFile}" 20 --CHART_OUTPUT '${pdfFile}'
22 CHART_OUTPUT="${pdfFile}" 21 --REFERENCE_SEQUENCE '${reference_fasta_filename}'
23 REFERENCE_SEQUENCE="${reference_fasta_filename}" 22 --ALIGNED_READS_ONLY '${aligned_reads_only}'
24 ALIGNED_READS_ONLY="${aligned_reads_only}" 23 --PF_READS_ONLY '${pf_reads_only}'
25 PF_READS_ONLY="${pf_reads_only}"
26 24
27 ASSUME_SORTED="${assume_sorted}" 25 --ASSUME_SORTED '${assume_sorted}'
28 26
29 VALIDATION_STRINGENCY="${validation_stringency}" 27 --VALIDATION_STRINGENCY '${validation_stringency}'
30 QUIET=true 28 --QUIET true
31 VERBOSITY=ERROR 29 --VERBOSITY ERROR
32 30
33 ]]></command> 31 ]]></command>
34 <inputs> 32 <inputs>
35 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> 33 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
36 <conditional name="reference_source"> 34 <conditional name="reference_source">
37 <param name="reference_source_selector" type="select" label="Load reference genome from"> 35 <param name="reference_source_selector" type="select" label="Load reference genome from">
38 <option value="cached">Local cache</option> 36 <option value="cached">Local cache</option>
39 <option value="history">History</option> 37 <option value="history">History</option>
40 </param> 38 </param>
41 <when value="cached"> 39 <when value="cached">
42 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> 40 <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
43 <options from_data_table="all_fasta"> 41 <options from_data_table="all_fasta">
44 </options> 42 </options>
45 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 43 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
46 </param> 44 </param>
47 </when> 45 </when>
48 <when value="history"> 46 <when value="history">
49 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> 47 <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference"/>
50 </when> 48 </when>
51 </conditional> 49 </conditional>
52 <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/> 50 <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/>
53 <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/> 51 <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/>
54 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> 52 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
55 53 <expand macro="VS"/>
56 <expand macro="VS" /> 54 </inputs>
57 55 <outputs>
58 </inputs> 56 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
59 57 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
60 <outputs> 58 </outputs>
61 <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> 59 <tests>
62 <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> 60 <test>
63 </outputs> 61 <param name="assume_sorted" value="true"/>
64 62 <param name="aligned_reads_only" value="false"/>
65 <tests> 63 <param name="pf_reads_only" value="false"/>
66 <test> 64 <param name="reference_source_selector" value="history"/>
67 <param name="assume_sorted" value="true" /> 65 <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa"/>
68 <param name="aligned_reads_only" value="false" /> 66 <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam"/>
69 <param name="pf_reads_only" value="false" /> 67 <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
70 <param name="reference_source_selector" value="history" /> 68 </test>
71 <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa" /> 69 </tests>
72 <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam" /> 70 <help>
73 <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
74 </test>
75 </tests>
76
77
78 <help>
79 71
80 .. class:: infomark 72 .. class:: infomark
81 73
82 **Purpose** 74 **Purpose**
83 75
98 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True 90 AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True
99 91
100 @more_info@ 92 @more_info@
101 93
102 </help> 94 </help>
103 <expand macro="citations" /> 95 <expand macro="citations"/>
104 </tool> 96 </tool>