Mercurial > repos > andrea.furlani > impc_tools

annotate impc_tool.xml @ 0:4357848fb4e6 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
author andrea.furlani
date Thu, 09 Jun 2022 10:51:23 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
1 <tool id="IMPC_query_tool" name="IMPC" version="0.9.0">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
2 <description> query tool.</description>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
3 <requirements>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
4 <requirement type="package">requests</requirement>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
5 <requirement type="package">pandas</requirement>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
6 <requirement type="package">lxml</requirement>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
7 </requirements>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
8 <stdio>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
9 </stdio>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
10 <command>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
11 <![CDATA[python3 "$__tool_directory__/impc_tool.py"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
12 #if $query_type.selector == '7'
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
13 '$query_type.input' '$output' '$query_type.selector' '$query_type.head'
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
14 #else
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
15 #if $query_type.inp_q.inp_sel == 'str'
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
16 '$query_type.inp_q.input' '$output' '$query_type.selector' '$query_type.head' '$query_type.inp_q.inp_sel'
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
17 #else
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
18 '$query_type.inp_q.input' '$output' '$query_type.selector' '$query_type.head' '$query_type.inp_q.inp_sel' '$query_type.inp_q.sep'
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
19 #end if
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
20 #end if]]>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
21 </command>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
22 <inputs>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
23 <conditional name="query_type">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
24 <param name="selector" type="select" label="Select a query:">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
25 <option value="1">1 - Extract all measured phenotypes related to a gene</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
26 <option value="2">2 - Extract all genes having a particular phenotype or a set of phenotypes (e.g. relevant to a disease)</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
27 <option value="3">3 - Extract all phenotypes which are present in a particular gene set (e.g. genes together in a pathway)</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
28 <option value="4">4 - Extract images with a particular phenotype or a set of phenotypes</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
29 <option value="5">5 - Which parameters have been measured for a particular knockout</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
30 <option value="6">6 - Which parameters identified a significant finding for a particular knockout</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
31 <option value="7">7 - Full table of genes and all identified phenotypes, no input needed</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
32 <option value="8">8 - Extract all genes names and ID measured in a specific pipeline</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
33 <option value="9">9 - Extract all genes and corresponding phenotypes related to a particular phenotype major category (not working for now)</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
34 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
35 <when value="1">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
36 <conditional name="inp_q">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
37 <param name="inp_sel" type="select" label="Select the type of input">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
38 <option value="str">1 - Direct input</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
39 <option value="txt">2 - Txt file</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
40 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
41 <when value="str">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
42 <param name="input" type="text" label="Input gene:" help="Enter a single MGI gene id or gene symbol"/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
43 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
44 <when value="txt">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
45 <param name="input" type="data" format="data,tabular,txt" label="Input file:" help="Enter a txt file with the Gene MGI id or Gene Symbol."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
46 <param name="sep" type="select" label="Select the separator used in the file:">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
47 <option value="t">tab</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
48 <option value="s">single space</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
49 <option value=",">,</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
50 <option value=";">;</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
51 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
52 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
53 </conditional>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
54 <param name="head" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Choose if include the header in the output. The default value is True."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
55 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
56 <when value="2">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
57 <conditional name="inp_q">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
58 <param name="inp_sel" type="select" label="Select the type of input">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
59 <option value="str">1 - Direct input</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
60 <option value="txt">2 - Txt file</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
61 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
62 <when value="str">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
63 <param name="input" type="text" label="Input phenotype or set of phenotypes:" help="Enter a single MP term id or a list dividing each id with a comma (without spaces)"/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
64 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
65 <when value="txt">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
66 <param name="input" type="data" format="data,tabular,txt" label="Input file:" help="Enter a txt file with the MP terms."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
67 <param name="sep" type="select" label="Select the separator used in the file:">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
68 <option value="t">tab</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
69 <option value="s">single space</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
70 <option value=",">,</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
71 <option value=";">;</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
72 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
73 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
74 </conditional>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
75 <param name="head" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Choose if include the header in the output. The default value is True."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
76 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
77 <when value="3">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
78 <conditional name="inp_q">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
79 <param name="inp_sel" type="select" label="Select the type of input">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
80 <option value="str">1 - Direct input</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
81 <option value="txt">2 - Txt file</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
82 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
83 <when value="str">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
84 <param name="input" type="text" label="Input gene or set of genes:" help="Enter a single MGI gene id (or gene symbol) or a list dividing each id with a comma (without spaces)"/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
85 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
86 <when value="txt">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
87 <param name="input" type="data" format="data,tabular,txt" label="Input file:" help="Enter a txt file with the MP terms."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
88 <param name="sep" type="select" label="Select the separator used in the file:">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
89 <option value="t">tab</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
90 <option value="s">single space</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
91 <option value=",">,</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
92 <option value=";">;</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
93 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
94 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
95 </conditional>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
96 <param name="head" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Choose if include the header in the output. The default value is True."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
97 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
98 <when value="4">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
99 <conditional name="inp_q">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
100 <param name="inp_sel" type="select" label="Select the type of input">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
101 <option value="str">1 - Direct input</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
102 <option value="txt">2 - Txt file</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
103 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
104 <when value="str">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
105 <param name="input" type="text" label="Input phenotype or set of phenotypes:" help="Enter a single MP term id or a list dividing each id with a comma (without spaces)"/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
106 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
107 <when value="txt">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
108 <param name="input" type="data" format="data,tabular,txt" label="Input file:" help="Enter a txt file with the MP terms."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
109 <param name="sep" type="select" label="Select the separator used in the file:">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
110 <option value="t">tab</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
111 <option value="s">single space</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
112 <option value=",">,</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
113 <option value=";">;</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
114 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
115 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
116 </conditional>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
117 <param name="head" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Choose if include the header in the output. The default value is True."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
118 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
119 <when value="5">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
120 <conditional name="inp_q">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
121 <param name="inp_sel" type="select" label="Select the type of input">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
122 <option value="str">1 - Direct input</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
123 <option value="txt">2 - Txt file</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
124 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
125 <when value="str">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
126 <param name="input" type="text" label="Input gene:" help="Enter a single MGI gene id or gene symbol"/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
127 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
128 <when value="txt">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
129 <param name="input" type="data" format="data,tabular,txt" label="Input file:" help="Enter a txt file with a MGI id or a gene symbol."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
130 <param name="sep" type="select" label="Select the separator used in the file:">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
131 <option value="t">tab</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
132 <option value="s">single space</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
133 <option value=",">,</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
134 <option value=";">;</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
135 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
136 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
137 </conditional>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
138 <param name="head" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Choose if include the header in the output. The default value is True."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
139 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
140 <when value="6">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
141 <conditional name="inp_q">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
142 <param name="inp_sel" type="select" label="Select the type of input">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
143 <option value="str">1 - Direct input</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
144 <option value="txt">2 - Txt file</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
145 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
146 <when value="str">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
147 <param name="input" type="text" label="Input gene:" help="Enter a single MGI gene id or gene symbol"/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
148 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
149 <when value="txt">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
150 <param name="input" type="data" format="data,tabular,txt" label="Input file:" help="Enter a txt file with a MGI id or a gene symbol."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
151 <param name="sep" type="select" label="Select the separator used in the file:">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
152 <option value="t">tab</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
153 <option value="s">single space</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
154 <option value=",">,</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
155 <option value=";">;</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
156 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
157 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
158 </conditional>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
159 <param name="head" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Choose if include the header in the output. The default value is True."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
160 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
161 <when value="7">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
162 <param name="input" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Include genes without identified phenotypes?" help="Choose if include in the output table also those genes that have no registred phenotypes. By default they are excluded."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
163 <param name="head" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Choose if include the header in the output. The default value is True."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
164 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
165 <when value="8">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
166 <conditional name="inp_q">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
167 <param name="inp_sel" type="select" label="Select the type of input">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
168 <option value="str">1 - Direct input</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
169 <option value="txt">2 - Txt file</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
170 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
171 <when value="str">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
172 <param name="input" type="text" label="Input pipeline:" help="Enter a IMPC pipeline id"/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
173 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
174 <when value="txt">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
175 <param name="input" type="data" format="data,tabular,txt" label="Input file:" help="Enter a txt file with a IMPC pipeline id."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
176 <param name="sep" type="select" label="Select the separator used in the file:">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
177 <option value="t">tab</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
178 <option value="s">single space</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
179 <option value=",">,</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
180 <option value=";">;</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
181 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
182 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
183 </conditional>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
184 <param name="head" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Choose if include the header in the output. The default value is True."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
185 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
186 <when value="9">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
187 <conditional name="inp_q">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
188 <param name="inp_sel" type="select" label="Select the type of input">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
189 <option value="str">1 - Direct input</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
190 <option value="txt">2 - Txt file</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
191 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
192 <when value="str">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
193 <param name="input" type="text" label="Input id:" help="Enter a phenotypic category mp id"/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
194 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
195 <when value="txt">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
196 <param name="input" type="data" format="data,tabular,txt" label="Input file:" help="Enter a txt file with a phenotypic category mp id."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
197 <param name="sep" type="select" label="Select the separator used in the file:">
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
198 <option value="t">tab</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
199 <option value="s">single space</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
200 <option value=",">,</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
201 <option value=";">;</option>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
202 </param>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
203 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
204 </conditional>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
205 <param name="head" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Choose if include the header in the output. The default value is True."/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
206 </when>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
207 </conditional>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
208 </inputs>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
209 <outputs>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
210 <data format="tabular" name="output" label="${tool.name} query n° $query_type.selector"/>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
211 </outputs>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
212 <help><![CDATA[
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
213 **What it does**
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
214
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
215 With this tool, it is possible to submit various types of queries to the IMPC database.
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
216 Select the desired query from the drop down menu. As input both MGI ids or gene symbols are allowed (even mixed). If you want to input more than one id, separate them with a comma without spaces (eg: MGI:104636,MGI:104637). If a mixed input is retrieved, the order after the mapping will not be maintained.
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
217 The mapping is performed using **bioDBnet** Python package (https://biodbnet.abcc.ncifcrf.gov/). Note that if the mapping between the two types of ids doesn't retrieves a result, that id will not be included in the query input, resulting in an error if all of the ids are not mapped. The output will be a table containing the data.
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
218 For query 7 no inputs are required and you can choose if including genes without identified phenotypes or not.
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
219 For each query is possible to choose if include or not an header row. Note that not all tools have an option to remove it automatically. In this case the user will have to remove it using the tool "Remove beginning of a file".
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
220 The headers for each query are the following:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
221
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
222 **1-** MP term name, MP term ID
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
223
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
224 **2-** Gene accession id, Gene name, Gene bundle url
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
225
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
226 **3-** MP term, genes
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
227
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
228 **4-** External sample id, Gene symbol, Biological sample group, Sex, Colony id, Zygosity, Parameter name, Download url, Thumbnail url
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
229
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
230 **5-** Parameter name
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
231
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
232 **6-** Parameter name, p-value
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
233
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
234 **7-** Gene, Identified phenotypes
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
235
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
236 **8-** Gene accession id, Gene name
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
237
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
238 **9-** Gene accession id, Significant mp term id, Significant mp term name
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
239
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
240 **Citation**
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
241
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
242 If you use this tool in Galaxy, please cite Infrafrontier GmbH
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
243 ]]></help>
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty
andrea.furlani
parents:
diff changeset
244 </tool>