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comparison mQC.xml @ 0:525f558e318e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/ commit 27d64fdb96ed232851b1b29cd66250a682df6f18-dirty
author rnateam
date Fri, 29 Sep 2017 04:20:20 -0400
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1 <tool id="mqc" name="mQC" version="1.7">
2 <description>quality control of ribosome profiling mapping results</description>
3 <requirements>
4 <requirement type="package" version="1.7">mqc</requirement>
5 </requirements>
6 <command>
7 mQC.pl
8 --galaxy Y
9 --galaxytest $galaxytest
10 --experiment_name $exp_name
11 --cores $cores
12 --species $species
13 --ens_v $ensv
14 --unique $uniq
15 --mapper $mapper
16 --maxmultimap $maxmultimap
17 --ens_db "get"
18 --offset $offsetSelect.offset
19 --min_length_gd $min_l_gd
20 --max_length_gd $max_l_gd
21 --plotrpftool $plotrpftool
22 --outhtml $MappingQC_output
23 --outfolder $MappingQC_output.files_path
24
25 #if $inputtypeSelect.inputtype == "sam"
26 --samfile '$inputtypeSelect.samfile'
27 --galaxysam Y
28 #else if $inputtypeSelect.inputtype == "bam"
29 --samfile '$inputtypeSelect.bamfile'
30 --galaxysam N
31 #end if
32 #if $offsetSelect.offset == "from_file"
33 --offset_file $offsetSelect.offsetFile
34 #else if $offsetSelect.offset == "plastid"
35 #if $inputtypeSelect.inputtype == "sam"
36 --plastid_bam "convert"
37 #else if $inputtypeSelect.inputtype == "bam"
38 --plastid_bam $inputtypeSelect.bamfile
39 #end if
40 --min_length_plastid $offsetSelect.min_l_plastid
41 --max_length_plastid $offsetSelect.max_l_plastid
42 #end if
43
44 </command>
45 <inputs>
46 <param name="galaxytest" type="hidden" value="N"/>
47 <conditional name="inputtypeSelect">
48 <param name="inputtype" type="select" label="Select the format of your input data">
49 <option value="sam" selected="true">SAM format</option>
50 <option value="bam">BAM format</option>
51 </param>
52 <when value="sam">
53 <param name="samfile" type="data" format="sam" label="Choose the sam file on which you want to do quality control"/>
54 </when>
55 <when value="bam">
56 <param name="bamfile" type="data" format="bam" label="Choose the bam file on which you want to do quality control"/>
57 </when>
58 </conditional>
59 <param name="exp_name" type="text" label="Enter the experiment name"/>
60 <param name="cores" type="integer" size="5" value="5" label="Enter the number of cores to run the mapping quality control"/>
61 <param name="species" type="select" label="Select the species">
62 <option value="mouse">Mouse</option>
63 <option value="human" selected="true">Human</option>
64 <option value="fruitfly">Fruitfly</option>
65 </param>
66 <param name="ensv" type="integer" size="5" value="86" label="Enter the Ensembl database version"/>
67 <param name="uniq" type="select" label="Perform mQC with unique mapped reads only">
68 <option value="Y" selected="true">Yes</option>
69 <option value="N">No</option>
70 </param>
71 <param name="plotrpftool" type="select" label="Choose the style of the RPF phase plot">
72 <option value="grouped2D" selected="true">Grouped 2D bar chart</option>
73 <option value="pyplot3D">3D bar chart (may suffer from Escher effects)</option>
74 </param>
75 <param name="mapper" type="select" label="Which mapper is used to generate your SAM file?">
76 <option value="STAR" selected="true">STAR</option>
77 <option value="TopHat2">TopHat2</option>
78 <option value="HiSat2">HiSat2</option>
79 </param>
80 <param name="maxmultimap" value="16" type="integer" label="Only use alignments that mapped fewer times than this value"/>
81 <param name="min_l_gd" value="26" type="integer" label="Enter the minimum RPF length for gene distribution construction"/>
82 <param name="max_l_gd" value="34" type="integer" label="Enter the maximum RPF length for gene distribution construction"/>
83 <conditional name="offsetSelect">
84 <param name="offset" type="select" label="The way P-site offsets were determined">
85 <option value="standard" selected="true">Standard offsets</option>
86 <option value="plastid">Calculate offsets with plastid</option>
87 <option value="from_file">Offsets from custom file</option>
88 </param>
89 <when value="standard"/>
90 <when value="from_file">
91 <param name="offsetFile" type="data" format="tabular" label="Choose a text file with the offsets. Each line should be structured as RPF length - offset, seperated by a tab or a space" />
92 </when>
93 <when value="plastid">
94 <param name="min_l_plastid" value="22" type="integer" label="Enter the minimum RPF length for plastid offset calculation"/>
95 <param name="max_l_plastid" value="34" type="integer" label="Enter the maximum RPF length for plastid offset calculation"/>
96 </when>
97 </conditional>
98 </inputs>
99 <outputs>
100 <data format="html" name="MappingQC_output" label="HTML output" />
101 </outputs>
102 <tests>
103 <test>
104 <param name="galaxytest" value="Y"/>
105 <param name="inputtype" value="sam"/>
106 <param name="samfile" value="test_data_mESC.sam" ftype="sam"/>
107 <param name="exp_name" value="test_data_mESC"/>
108 <param name="cores" value="10"/>
109 <param name="species" value="mouse"/>
110 <param name="ensv" value="86"/>
111 <param name="uniq" value="Y"/>
112 <param name="plotrpftool" value="grouped2D"/>
113 <param name="mapper" value="STAR"/>
114 <param name="maxmultimap" value="16"/>
115 <param name="min_l_gd" value="26"/>
116 <param name="max_l_gd" value="34"/>
117 <param name="offset" value="standard"/>
118 <output name="MappingQC_output" file="mQC_test_data_mESC/mQC_test_data_mESC.html" ftype="html"/>
119 </test>
120 </tests>
121 <help>
122 .. class:: infomark
123
124 **What it does**
125
126 MappingQC is a tool to easily generate some figures which give a nice overview of the quality of the mapping of ribosome profiling data. More specific, it gives an overview of the P site offset calculation, the gene distribution and the metagenic classification. Furthermore, MappingQC does a thorough analysis of the triplet periodicity and the linked triplet phase (typical for ribosome profiling) in the canonical transcript of your data. Especially, the link between the phase distribution and the RPF length, the relative sequence position and the triplet identity are taken into account.
127
128 There is also a version from MappingQC available, which is directly linked to PROTEOFORMER and its SQLite results database structure. This makes its usage in combination with PROTEOFORMER more straight forward and can speed up the total analysis process.
129
130 -----
131
132 .. class:: infomark
133
134 **Input**
135
136 1) SAM file with mapping results
137
138 2) Ensembl DB with annotation for the selected species and Ensembl version
139
140 ------
141
142 .. class:: infomark
143
144 **Output**
145
146 1) HTML file: overview file of the tables and figures. Main output of MappingQC
147
148 2) ZIP file: contains a folder with all necessary figures. In this folder you can also find the overview HTML file.
149
150 </help>
151 <citations>
152 <citation type="bibtex">
153 @article{verbruggen_menschaert_2017, title={MappingQC: a tool for quality control of ribosome profiling mapping results}, journal={Unpublished}, author={Verbruggen, Steven and Menschaert, Gerben}, year={2017}}
154 </citation>
155 </citations>
156 </tool>