filter_keywords_values: filter_kw

annotate filter_kw_val.xml @ 5:1e9911190142 draft

planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty

author	proteore
date	Wed, 14 Mar 2018 10:24:54 -0400
parents	2c1012e0a628
children	6f32c1e12572

rev	line source
3 593b8a1b2a7b planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty proteore parents: 2 diff changeset	1 <tool id="MQoutputfilter" name="Filter by keywords or numerical value" version="0.1.0">
4 2c1012e0a628 planemo upload commit f23adbff4edf77bde1fe742f7bd6dcc7ae0fbb8e-dirty proteore parents: 3 diff changeset	2 <description></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" >
5 1e9911190142 planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty proteore parents: 4 diff changeset	58 <param name="txt" type="text" label="Copy/paste keywords to be filtered out" 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 ${input1.name}" />
5 1e9911190142 planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty proteore parents: 4 diff changeset	109 <data name="trash_file" format="tabular" label="${tool.name} on ${input1.name} - Filtered 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[
5 1e9911190142 planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty proteore parents: 4 diff changeset	128 This tool allows to filter out data according to your specific needs (e.g. contaminants, non-significant values or related to a particular annotation) from a proteomics results file (e.g. MaxQuant or Proline output).
0 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
5 1e9911190142 planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty proteore parents: 4 diff changeset	146 The line that contains these keywords will be filtered from input file and provided in a separate 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
5 1e9911190142 planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty proteore parents: 4 diff changeset	150 - If you choose Yes, only the fields that contains exactly the same content will be filtered.
1 d29e469b6b20 planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty proteore parents: 0 diff changeset	151
5 1e9911190142 planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty proteore parents: 4 diff changeset	152 - If you choose No, all the fields containing the keyword will be filtered.
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
5 1e9911190142 planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty proteore parents: 4 diff changeset	156 Yes option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is filtered (and not "Kinase").
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
5 1e9911190142 planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty proteore parents: 4 diff changeset	172 * A text file containing the rows that have been filtered 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>

Mercurial > repos > proteore > filter_keywords_values

annotate filter_kw_val.xml @ 5:1e9911190142 draft