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comparison rseqc_macros.xml @ 51:09846d5169fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author iuc
date Tue, 14 Mar 2017 10:23:21 -0400
parents 6b33e31bda10
children 34e4c586e3c0
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50:f242ee103277 51:09846d5169fa
1 <macros> 1 <macros>
2 2
3 <xml name="requirement_package_r"><requirement type="package" version="3.0.3">R</requirement></xml> 3 <token name="@WRAPPER_VERSION@">2.6.4</token>
4 <xml name="requirement_package_numpy"><requirement type="package" version="1.7.1">numpy</requirement></xml> 4
5 <xml name="requirement_package_rseqc"><requirement type="package" version="2.4">rseqc</requirement></xml> 5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="2.6.4">rseqc</requirement>
8 </requirements>
9 </xml>
6 10
7 <xml name="stdio"> 11 <xml name="stdio">
8 <stdio> 12 <stdio>
9 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 13 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
10 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 14 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
11 </stdio> 15 </stdio>
12 </xml> 16 </xml>
13 17
18 <!-- Params -->
19 <xml name="bam_param">
20 <param name="input" type="data" label="Input .bam file" format="bam" help="(--input-file)"/>
21 </xml>
22
23 <xml name="bam_sam_param">
24 <param name="input" type="data" label="Input .bam/.sam file" format="bam,sam" help="(--input-file)"/>
25 </xml>
26
27 <xml name="refgene_param">
28 <param name="refgene" type="data" format="bed" label="Reference gene model" help="(--refgene)"/>
29 </xml>
30
31 <xml name="mapq_param">
32 <param name="mapq" type="integer" label="Minimum mapping quality" value="30" help="Minimum mapping quality for an alignment to be considered as &quot;uniquely mapped&quot; (--mapq)"/>
33 </xml>
34
35 <xml name="readlength_param">
36 <param name="readlength" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length (--read-align-length)"/>
37 </xml>
38
39 <xml name="readnum_param">
40 <param name="readnum" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile (--read-num)"/>
41 </xml>
42
43 <xml name="sample_size_param">
44 <param name="sample_size" type="integer" label="Number of reads sampled from SAM/BAM file (default = 200000)" value="200000" min="1" help="(--sample-size)"/>
45 </xml>
46
47 <xml name="min_intron_param">
48 <param name="min_intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" help="(--min-intron)" />
49 </xml>
50
51 <xml name="layout_param">
52 <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)">
53 <option value="SE" selected="true">Single-end</option>
54 <option value="PE">Paired-end</option>
55 </param>
56 </xml>
57
58 <xml name="strand_type_param">
59 <conditional name="strand_type">
60 <param name="strand_specific" type="select" label="Strand-specific?">
61 <option value="none" selected="true">None</option>
62 <option value="pair">Pair-End RNA-seq</option>
63 <option value="single">Single-End RNA-seq</option>
64 </param>
65 <when value="pair">
66 <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" help="(--strand)">
67 <option value="sd" selected="true"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option>
68 <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option>
69 </param>
70 </when>
71 <when value="single">
72 <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" help="(--strand)">
73 <option value="s" selected="true">positive --> positive; negative --> negative</option>
74 <option value="d">positive --> negative; negative --> positive</option>
75 </param>
76 </when>
77 <when value="none"></when>
78 </conditional>
79 </xml>
80
81 <xml name="multihits_param">
82 <conditional name="multihits_type">
83 <param name="multihits_type_selector" type="select" label="Reads with multiple hits" help="(--skip-multi-hits)">
84 <option value="use_multihits" selected="true">Count Mutliple Hit Reads</option>
85 <option value="skip_multihits">Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads</option>
86 </param>
87 <when value="skip_multihits">
88 <expand macro="mapq_param" />
89 </when>
90 <when value="use_multihits" />
91 </conditional>
92 </xml>
93
94 <xml name="rscript_output_param">
95 <param name="rscript_output" type="boolean" value="false" label="Output R-Script"
96 help="Output the R-Script used to generate the plots" />
97 </xml>
98
99
100 <!-- Output -->
101
102 <xml name="pdf_output_data" token_filename="output.pdf">
103 <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (pdf)" />
104 </xml>
105
106 <xml name="xls_output_data" token_filename="output.xls">
107 <data format="xls" name="outputxls" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (xls)" />
108 </xml>
109
110 <xml name="rscript_output_data" token_filename="output.r">
111 <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="${tool.name} on ${on_string} (rscript)">
112 <filter>rscript_output</filter>
113 </data>
114 </xml>
115
116 <!-- Command -->
117 <token name="@MULTIHITS@">
118 <![CDATA[
119 #if str($multihits_type.multihits_type_selector) == "skip_multihits"
120 --skip-multi-hits
121 --mapq=${multihits_type.mapq}
122 #end if
123 ]]>
124 </token>
125
126 <token name="@ABOUT@">
127
128 -----
129
130 About RSeQC
131 +++++++++++
132
133 The RSeQC_ package provides a number of useful modules that can comprehensively
134 evaluate high throughput sequence data especially RNA-seq data. "Basic modules"
135 quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC
136 bias, while "RNA-seq specific modules" investigate sequencing saturation status
137 of both splicing junction detection and expression estimation, mapped reads
138 clipping profile, mapped reads distribution, coverage uniformity over gene
139 body, reproducibility, strand specificity and splice junction annotation.
140
141 The RSeQC package is licensed under the GNU GPL v3 license.
142
143 .. image:: $PATH_TO_IMAGES/logo.png
144
145 .. _RSeQC: http://rseqc.sourceforge.net/
146
147
148 </token>
149
14 <xml name="citations"> 150 <xml name="citations">
15 <citations> 151 <citations>
16 <citation type="bibtex"> 152 <citation type="doi">10.1093/bioinformatics/bts356</citation>
17 @article{wang_rseqc:_2012,
18 title = {{RSeQC}: quality control of {RNA}-seq experiments},
19 volume = {28},
20 issn = {1367-4803, 1460-2059},
21 shorttitle = {{RSeQC}},
22 url = {http://bioinformatics.oxfordjournals.org/content/28/16/2184},
23 doi = {10.1093/bioinformatics/bts356},
24 abstract = {Motivation: RNA-seq has been extensively used for transcriptome study. Quality control (QC) is critical to ensure that RNA-seq data are of high quality and suitable for subsequent analyses. However, QC is a time-consuming and complex task, due to the massive size and versatile nature of RNA-seq data. Therefore, a convenient and comprehensive QC tool to assess RNA-seq quality is sorely needed.
25 Results: We developed the RSeQC package to comprehensively evaluate different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity and read distribution over the genome structure. RSeQC takes both SAM and BAM files as input, which can be produced by most RNA-seq mapping tools as well as BED files, which are widely used for gene models. Most modules in RSeQC take advantage of R scripts for visualization, and they are notably efficient in dealing with large BAM/SAM files containing hundreds of millions of alignments.
26 Availability and implementation: RSeQC is written in Python and C. Source code and a comprehensive user's manual are freely available at: http://code.google.com/p/rseqc/.
27 Contact: WL1\{at\}bcm.edu
28 Supplementary Information: Supplementary data are available at Bioinformatics online.},
29 language = {en},
30 number = {16},
31 urldate = {2015-06-30},
32 journal = {Bioinformatics},
33 author = {Wang, Liguo and Wang, Shengqin and Li, Wei},
34 month = aug,
35 year = {2012},
36 pmid = {22743226},
37 pages = {2184--2185},
38 }
39 </citation>
40 </citations> 153 </citations>
41 </xml> 154 </xml>
42 </macros> 155 </macros>