Mercurial > repos > proteore > filter_keywords_values
annotate filter_kw_val.xml @ 2:330d6c7b1916 draft
planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
author | proteore |
---|---|
date | Thu, 01 Mar 2018 08:15:55 -0500 |
parents | d29e469b6b20 |
children | 593b8a1b2a7b |
rev | line source |
---|---|
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
1 <tool id="MQoutputfilter" name="Filter lines by keywords or numerical value" version="0.1.0"> |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
2 <description>Filter a file by keywords or numerical values</description> |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
3 <requirements> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
4 </requirements> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
5 <stdio> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
6 <exit_code range="1:" /> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
7 </stdio> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
8 <command><![CDATA[ |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
9 python $__tool_directory__/filter_kw_val.py |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
10 -i "$input1,$header" |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
11 -o "$output1" |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
12 --trash_file "$trash_file" |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
13 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
14 ## Keywords |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
15 #for $i, $key in enumerate($keyword) |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
16 #if $key.k.kw != "None" |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
17 #if $key.k.kw == "text" |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
18 --kw "$key.k.txt" "$key.ncol" "$key.match" |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
19 #else if $key.k.kw == "file" |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
20 --kw_file "$key.k.file" "$key.ncol" "$key.match" |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
21 #end if |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
22 #end if |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
23 #end for |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
24 |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
25 ## Number of proteins |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
26 #for $i, $val in enumerate($value) |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
27 #if $val.v.val != "None" |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
28 --value |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
29 #if $val.v.val == "Equal" |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
30 $val.v.equal "$val.ncol" "=" |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
31 #else if $val.v.val == "Higher" |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
32 $val.v.higher "$val.ncol" ">" |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
33 #else if $val.v.val == "Equal or higher" |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
34 $val.v.equal_higher "$val.ncol" ">=" |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
35 #else if $val.v.val == "Lower" |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
36 $val.v.lower "$val.ncol" "<" |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
37 #else |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
38 $val.v.equal_lower "$val.ncol" "<=" |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
39 #end if |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
40 #end if |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
41 #end for |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
42 |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
43 ]]></command> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
44 <inputs> |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
45 <param type="data" name="input1" format="txt,tabular" label="Input file" help="Input file is a tab-delimited file containing proteomics identification and/or quantitative results" /> |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
46 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
47 <repeat name="keyword" title="Filter by keywords" > |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
48 <param name="ncol" type="text" value="c1" label="Please specify the column number of the input file on which you want to apply the filter" help='For example, fill in "c1" if the keywords you want to filter out are listed in the first column' /> |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
49 <param type="boolean" name="match" truevalue="True" label="Would you like to search for exact match?" help='Choosing "Yes" will only filter out exact match (i.e. case sensitive), see below for more details' /> |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
50 <conditional name="k" > |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
51 <param argument="--kw" type="select" label="Filter by keyword" > |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
52 <option value="None" selected="True">---</option> |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
53 <option value="text">Enter keywords (copy/paste)</option> |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
54 <option value="file">Choose a file containing keywords</option> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
55 </param> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
56 <when value="None" /> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
57 <when value="text" > |
2
330d6c7b1916
planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
1
diff
changeset
|
58 <param name="txt" type="text" label="Copy/paste keywords to be removed" help='Keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175' > |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
59 <sanitizer> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
60 <valid initial="string.printable"> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
61 <remove value="'"/> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
62 </valid> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
63 <mapping initial="none"> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
64 <add source="'" target="__sq__"/> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
65 </mapping> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
66 </sanitizer> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
67 </param> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
68 </when> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
69 <when value="file" > |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
70 <param name="file" type="data" format="txt,tabular" label="Choose a file containing keywords" /> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
71 </when> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
72 </conditional> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
73 </repeat> |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
74 |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
75 <repeat name="value" title="Filter by value" > |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
76 <param name="ncol" type="text" value="c1" label="Please specify the column number of the input file on which you want to apply the filter" help='For example, fill in "c1" if the keywords you want to filter out are listed in the first column' /> |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
77 <conditional name="v" > |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
78 <param argument="--val" type="select" label="Filter by value" > |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
79 <option value="None">---</option> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
80 <option value="Equal">=</option> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
81 <option value="Higher">></option> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
82 <option value="Equal or higher">>=</option> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
83 <option value="Lower"><</option> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
84 <option value="Equal or lower"><=</option> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
85 </param> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
86 <when value="None" > |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
87 </when> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
88 <when value="Equal" > |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
89 <param name="equal" type="float" value="" label="Value" /> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
90 </when> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
91 <when value="Higher" > |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
92 <param type="float" name="higher" value="" label="Value" /> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
93 </when> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
94 <when value="Equal or higher" > |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
95 <param type="float" name="equal_higher" value="" label="Value" /> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
96 </when> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
97 <when value="Lower" > |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
98 <param type="float" name="lower" value="" label="Value" /> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
99 </when> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
100 <when value="Equal or lower" > |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
101 <param type="float" name="equal_lower" value="" label="Value" /> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
102 </when> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
103 </conditional> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
104 </repeat> |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
105 |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
106 </inputs> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
107 <outputs> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
108 <data name="output1" format="tabular" label="${tool.name} on ${input1.name}" /> |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
109 <data name="trash_file" format="tabular" label="${tool.name} on ${input1.name} - Removed lines" /> |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
110 </outputs> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
111 <tests> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
112 <test> |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
113 <param name="input1" value="Lacombe_et_al_2017_OK.txt" /> |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
114 <param name="header" value="true" /> |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
115 <repeat name="keyword"> |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
116 <param name="ncol" value="c1" /> |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
117 <param name="match" value="True" /> |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
118 <conditional name="k"> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
119 <param name="kw" value="text" /> |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
120 <param name="txt" value="P04264;P35908;P13645;Q5D862;Q5T749;Q8IW75;P81605;P22531;P59666;P78386" /> |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
121 </conditional> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
122 </repeat> |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
123 <output name="output1" file="FKW_Lacombe_et_al_2017_OK.txt" /> |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
124 <output name="trash_file" file="Trash_FKW_Lacombe_et_al_2017_OK.txt" /> |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
125 </test> |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
126 </tests> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
127 <help><![CDATA[ |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
128 This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output). |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
129 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
130 **For each row, if there are more than one protein IDs/protein names/gene names, only the first one will be considered in the output** |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
131 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
132 **Filter the file by keywords** |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
133 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
134 Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords. |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
135 |
2
330d6c7b1916
planemo upload commit ffa3be72b850aecbfbd636de815967c06a8f643f-dirty
proteore
parents:
1
diff
changeset
|
136 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175 |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
137 |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
138 - If you choose to upload a file in a text format in which each line is a keyword, for example: |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
139 |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
140 REV |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
141 |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
142 TRYP_PIG |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
143 |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
144 ALDOA_RABBIT |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
145 |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
146 **The line that contains these keywords will be eliminated from input file.** |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
147 |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
148 **Keywords search can be applied by performing either exact match or partial one by using the following option** |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
149 |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
150 - If you choose **Yes**, only the fields that contains exactly the same content will be removed. |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
151 |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
152 - If you choose **No**, all the fields containing the keyword will be removed. |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
153 |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
154 For example: |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
155 |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
156 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed. |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
157 |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
158 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed. |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
159 |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
160 **Filter the file by values** |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
161 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
162 You can choose to use one or more options (e.g. to filter out peptides of low intensity value, by q-value, etc.). |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
163 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
164 * For each option, you can choose between "=", ">", ">=", "<" and "<=", then enter the value to filter and specify the column to apply that option. |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
165 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
166 **Output** |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
167 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
168 The tool will produce 2 output files. |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
169 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
170 * A text file containing the resulting filtered input file. |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
171 |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
172 * A text file containing the rows removed from the input file. |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
173 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
174 ----- |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
175 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
176 .. class:: infomark |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
177 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
178 **Authors** |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
179 |
1
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
180 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
181 |
d29e469b6b20
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
proteore
parents:
0
diff
changeset
|
182 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR |
0
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
183 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
184 This work has been partially funded through the French National Agency for Research (ANR) IFB project. |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
185 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
186 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
187 |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
188 ]]></help> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
189 <citations> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
190 </citations> |
6a45ccfc0e4c
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
proteore
parents:
diff
changeset
|
191 </tool> |