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comparison xpore_diffmod.xml @ 0:b64b9a2bf4f0 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore commit 617026dab446713793b40d5556aac16180e68eea"
author artbio
date Wed, 26 May 2021 23:14:24 +0000
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children ff53cf0d0bbd
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-1:000000000000 0:b64b9a2bf4f0
1 <tool id="xpore_diffmod" name="xpore-diffmod" version="0.5.6+galaxy1">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.5.6">xpore</requirement>
5 <requirement type="package" version="1.9.0">pyensembl</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" level="fatal" description="Tool exception" />
9 </stdio>
10 <command detect_errors="exit_code"><![CDATA[
11 printf "notes: Pairwise comparison without replicates with default parameter setting.\n\n" >> config.yml &&
12 printf "data:\n" >> config.yml &&
13 printf " ${control_name}:\n" >> config.yml &&
14 #for $i, $s in enumerate($ControlReplicates):
15 printf " rep${i}: ./${control_name}_${i}\n" >> config.yml &&
16 mkdir ${control_name}_${i} &&
17 ln -s ${s.ControlJson} ${control_name}_${i}/data.json &&
18 ln -s ${s.ControlIndex} ${control_name}_${i}/data.index &&
19 ln -s ${s.ControlReadcount} ${control_name}_${i}/data.readcount &&
20 #end for
21 printf " ${test_name}:\n" >> config.yml &&
22 #for $i, $s in enumerate($TestReplicates):
23 printf " rep${i}: ./${test_name}_${i}\n" >> config.yml &&
24 mkdir ${test_name}_${i} &&
25 ln -s ${s.TestJson} ${test_name}_${i}/data.json &&
26 ln -s ${s.TestIndex} ${test_name}_${i}/data.index &&
27 ln -s ${s.TestReadcount} ${test_name}_${i}/data.readcount &&
28 #end for
29 printf "\nout: ./out\n" >> config.yml &&
30 printf "\nmethod:\n" >> config.yml &&
31 printf " prefiltering:\n" >> config.yml &&
32 printf " method: t-test\n" >> config.yml &&
33 printf " threshold: 0.1\n" >> config.yml &&
34
35 xpore-diffmod --config config.yml --n_processes \${GALAXY_SLOTS:-4} &&
36 sed -i "s/,/\t/g" ./out/diffmod.table
37
38 ]]></command>
39 <inputs>
40 <param name="control_name" type="text" label="Control condition name"
41 help="Only letters, digits and _ will be retained in this field">
42 <sanitizer>
43 <valid initial="string.letters,string.digits"><add value="_" /></valid>
44 </sanitizer>
45 </param>
46 <repeat name="ControlReplicates" title="Control replicates" min="1">
47 <param name="ControlJson" label="json from xpore-dataprep" type="data" format="json" />
48 <param name="ControlIndex" label="index from xpore-dataprep" type="data" format="txt" />
49 <param name="ControlReadcount" label="Readcount from xpore-dataprep" type="data" format="txt" />
50 </repeat>
51
52 <param name="test_name" type="text" label="Test condition name"
53 help="Only letters, digits and _ will be retained in this field">
54 <sanitizer>
55 <valid initial="string.letters,string.digits"><add value="_" /></valid>
56 </sanitizer>
57 </param>
58 <repeat name="TestReplicates" title="Test replicates" min="1">
59 <param name="TestJson" label="json from xpore-dataprep" type="data" format="json" />
60 <param name="TestIndex" label="index from xpore-dataprep" type="data" format="txt" />
61 <param name="TestReadcount" label="Readcount from xpore-dataprep" type="data" format="txt" />
62 </repeat>
63
64 </inputs>
65
66 <outputs>
67 <data format="tabular" name="diffmod_table" label="diffmod table" from_work_dir="./out/diffmod.table" />
68 <data format="txt" name="diffmod_log" label="diffmod log" from_work_dir="./out/diffmod.log" />
69 <data format="txt" name="config" label="configuration.yml" from_work_dir="./config.yml" />
70 </outputs>
71 <tests>
72 <test>
73 <param name="control_name" value="control" />
74 <repeat name="ControlReplicates">
75 <param name="ControlJson" value="inputs_xpore-diffmod/C1_data.json" ftype="json" />
76 <param name="ControlIndex" value="inputs_xpore-diffmod/C1_data.index" ftype="txt" />
77 <param name="ControlReadcount" value="inputs_xpore-diffmod/C1_data.readcount" />
78 </repeat>
79 <repeat name="ControlReplicates">
80 <param name="ControlJson" value="inputs_xpore-diffmod/C2_data.json" ftype="json" />
81 <param name="ControlIndex" value="inputs_xpore-diffmod/C2_data.index" ftype="txt" />
82 <param name="ControlReadcount" value="inputs_xpore-diffmod/C2_data.readcount" ftype="txt" />
83 </repeat>
84 <param name="test_name" value="test" />
85 <repeat name="TestReplicates">
86 <param name="TestJson" value="inputs_xpore-diffmod/T1_data.json" ftype="json"/>
87 <param name="TestIndex" value="inputs_xpore-diffmod/T1_data.index" ftype="txt" />
88 <param name="TestReadcount" value="inputs_xpore-diffmod/T1_data.readcount" ftype="txt" />
89 </repeat>
90 <repeat name="TestReplicates">
91 <param name="TestJson" value="inputs_xpore-diffmod/T2_data.json" ftype="json"/>
92 <param name="TestIndex" value="inputs_xpore-diffmod/T2_data.index" ftype="txt" />
93 <param name="TestReadcount" value="inputs_xpore-diffmod/T2_data.readcount" ftype="txt" />
94 </repeat>
95 <output file="diffmod.table" name="diffmod_table" ftype="tabular" compare="sim_size" delta="400" />
96 <output file="diffmod.log" name="diffmod_log" ftype="txt" />
97 </test>
98 </tests>
99 <help>
100
101 **What it does**
102
103 This tool is a basic wrapper of xpore-diffmod for analysis of differential RNA modification
104 across all tested positions.
105
106 .. class:: warningmark
107
108 In its current version, only the analysis based on a transcripts collection reference is
109 implemented.
110
111 **Inputs**
112
113 You need 3 input datasets generated by the tool xpore-dataprep::
114
115 - data.index
116 - data.json
117 - data.readcount
118
119
120 **Output**
121
122 - a diffmod_table of the differential RNA modifications across all tested positions of transcripts
123 - a diffmod.log of the analysis
124
125 for details on xpore-diffmod, see https://xpore.readthedocs.io/en/latest/index.html
126 and https://github.com/GoekeLab/xpore
127
128
129 </help>
130
131 <citations>
132 <citation type="doi">10.1101/2020.06.18.160010</citation>
133 </citations>
134 </tool>