proteore_filter_keywords_values: filter_kw

annotate filter_kw_val.xml @ 1:cb9555653b09 draft

planemo upload commit 576387120daa98b935be56dc7ae62b9bf1e8a7ff-dirty

author	proteore
date	Fri, 21 Sep 2018 06:03:25 -0400
parents	a55e8b137c6b
children	52a7afd01c6d

rev	line source
1 cb9555653b09 planemo upload commit 576387120daa98b935be56dc7ae62b9bf1e8a7ff-dirty proteore parents: 0 diff changeset	1 <tool id="MQoutputfilter" name="Filter by keywords or numerical value" version="2018.09.21">
0 a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	2 <description></description>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	3 <requirements>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	4 </requirements>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	5 <stdio>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	6 <exit_code range="1:" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	7 </stdio>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	8 <command><![CDATA[
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	9 python $__tool_directory__/filter_kw_val.py
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	10 -i "$input1,$header"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	11 -o "$output1"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	12 --filtered_file "$filtered_file"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	13 --operator "$operator"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	14
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	15 ## Keywords
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	16 #for $key in $keyword
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	17 #if $key.k.kw != "None"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	18 #if $key.k.kw == "text"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	19 --kw "$key.k.txt" "$key.ncol" "$key.match"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	20 #else if $key.k.kw == "file"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	21 --kw_file "$key.k.file" "$key.ncol" "$key.match"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	22 #end if
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	23 #end if
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	24 #end for
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	25
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	26 ## value to filter
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	27 #for $val in $value
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	28 #if $val.v.val != "None"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	29 --value
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	30 #if $val.v.val == "Equal"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	31 $val.v.equal "$val.ncol" "="
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	32 #else if $val.v.val == "Higher"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	33 $val.v.higher "$val.ncol" ">"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	34 #else if $val.v.val == "Equal or higher"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	35 $val.v.equal_higher "$val.ncol" ">="
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	36 #else if $val.v.val == "Lower"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	37 $val.v.lower "$val.ncol" "<"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	38 #else if $val.v.val == "Equal or lower"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	39 $val.v.equal_lower "$val.ncol" "<="
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	40 #else
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	41 $val.v.different "$val.ncol" "!="
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	42 #end if
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	43 #end if
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	44 #end for
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	45
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	46 ##range of values to keep
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	47 #for $vr in $values_range
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	48 #if vr
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	49 --values_range $vr.bottom_value $vr.top_value $vr.ncol $vr.inclusive
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	50 #end if
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	51 #end for
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	52
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	53 #if $sort_column != ""
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	54 --sort_col "$sort_column,$reversed_sort"
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	55 #end if
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	56
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	57 ]]></command>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	58 <inputs>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	59 <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" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	60 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
1 cb9555653b09 planemo upload commit 576387120daa98b935be56dc7ae62b9bf1e8a7ff-dirty proteore parents: 0 diff changeset	61 <param name="operator" type="select" label="Please select an operator to combine your filters (if more than one)" help="OR : only one filter must be satisfied to filter a row, AND : all your filters must be satisfied to filter a row" >
0 a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	62 <option value="OR" selected="True">OR</option>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	63 <option value="AND">AND</option>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	64 </param>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	65 <param name="sort_column" type="text" value="" label="If you want to sort the result files by values from a column, please enter a column number" help="For example : fill in 'c1' if you want to sort your result file by the column 1 values." />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	66 <param name="reversed_sort" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Sort in descending order ?"/>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	67 <repeat name="keyword" title="Filter by keywords" >
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	68 <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' />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	69 <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' />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	70 <conditional name="k" >
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	71 <param argument="--kw" type="select" label="Filter by keyword" >
1 cb9555653b09 planemo upload commit 576387120daa98b935be56dc7ae62b9bf1e8a7ff-dirty proteore parents: 0 diff changeset	72 <option value="text" selected="true">Enter keywords (copy/paste)</option>
0 a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	73 <option value="file">Choose a file containing keywords</option>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	74 </param>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	75 <when value="None" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	76 <when value="text" >
1 cb9555653b09 planemo upload commit 576387120daa98b935be56dc7ae62b9bf1e8a7ff-dirty proteore parents: 0 diff changeset	77 <param name="txt" type="text" label="Copy/paste keywords to be filtered out" help='Keywords must be separated by ";", for example: A8K2U0;Q5TA79;O43175' >
0 a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	78 <sanitizer>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	79 <valid initial="string.printable">
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	80 <remove value="'"/>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	81 </valid>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	82 <mapping initial="none">
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	83 <add source="'" target="__sq__"/>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	84 </mapping>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	85 </sanitizer>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	86 </param>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	87 </when>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	88 <when value="file" >
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	89 <param name="file" type="data" format="txt,tabular" label="Choose a file containing keywords" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	90 </when>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	91 </conditional>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	92 </repeat>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	93 <repeat name="value" title="Filter by value" >
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	94 <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' />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	95 <conditional name="v" >
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	96 <param argument="--val" type="select" label="Filter by value" >
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	97 <option value="None">---</option>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	98 <option value="Equal">=</option>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	99 <option value="Higher">></option>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	100 <option value="Equal or higher">>=</option>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	101 <option value="Lower"><</option>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	102 <option value="Equal or lower"><=</option>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	103 <option value="Different">!=</option>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	104 </param>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	105 <when value="None" >
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	106 </when>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	107 <when value="Equal" >
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	108 <param name="equal" type="float" value="" label="Value" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	109 </when>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	110 <when value="Higher" >
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	111 <param type="float" name="higher" value="" label="Value" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	112 </when>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	113 <when value="Equal or higher" >
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	114 <param type="float" name="equal_higher" value="" label="Value" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	115 </when>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	116 <when value="Lower" >
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	117 <param type="float" name="lower" value="" label="Value" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	118 </when>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	119 <when value="Equal or lower" >
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	120 <param type="float" name="equal_lower" value="" label="Value" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	121 </when>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	122 <when value="Different">
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	123 <param type="float" name="different" value="" label="Value"/>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	124 </when>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	125 </conditional>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	126 </repeat>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	127 <repeat name="values_range" title="Filter by range of values">
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	128 <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' />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	129 <param name="bottom_value" type="float" value="" label="Please enter the bottom value" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	130 <param name="top_value" type="float" value="" label="Please enter the top value" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	131 <param name="inclusive" type="boolean" label="inclusive range ?" checked="false" truevalue="true" falsevalue="false" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	132 </repeat>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	133 </inputs>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	134 <outputs>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	135 <data name="output1" format="tabular" label="${tool.name} on ${input1.name}" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	136 <data name="filtered_file" format="tabular" label="${tool.name} on ${input1.name} - Filtered lines" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	137 </outputs>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	138 <tests>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	139 <test>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	140 <param name="input1" value="Lacombe_et_al_2017_OK.txt" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	141 <param name="header" value="true" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	142 <param name="operator" value="OR"/>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	143 <param name="sort_column" value="c1"/>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	144 <param name="reversed_sort" value="false"/>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	145 <repeat name="keyword">
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	146 <param name="ncol" value="c1" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	147 <param name="match" value="True" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	148 <conditional name="k">
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	149 <param name="kw" value="text" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	150 <param name="txt" value="P04264;P35908;P13645;Q5D862;Q5T749;Q8IW75;P81605;P22531;P59666;P78386" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	151 </conditional>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	152 </repeat>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	153 <repeat name="value">
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	154 <param name="ncol" value="c3"/>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	155 <conditional name="v">
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	156 <param name="val" value="Higher"/>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	157 <param name="higher" value="20" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	158 </conditional>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	159 </repeat>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	160 <output name="output1" file="output.csv" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	161 <output name="filtered_file" file="filtered_output.csv" />
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	162 </test>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	163 </tests>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	164 <help><![CDATA[
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	165 This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output).
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	166
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	167 Filter by keyword(s)
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	168
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	169 Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords.
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	170
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	171 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	172
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	173 - If you choose to upload a file in a text format in which each line is a keyword, for example:
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	174
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	175 REV
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	176
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	177 TRYP_PIG
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	178
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	179 ALDOA_RABBIT
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	180
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	181 The line that contains these keywords will be eliminated from input file.
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	182
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	183 Keywords search can be applied by performing either exact match or partial one by using the following option
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a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	185 - If you choose Yes, only the fields that contains exactly the same content will be removed.
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a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	187 - If you choose No, all the fields containing the keyword will be removed.
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	188
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	189 For example:
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	190
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	191 Yes option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed.
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	192
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	193 No option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed.
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a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	195 -----
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	196
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	197 Filter by values
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	198
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	199 You can filter your data by a column of numerical values.
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	200 Enter the column to be use and select one operator in the list :
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	201
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	202 - =
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	203 - !=
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	204 - <
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	205 - <=
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	206 - >
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	207 - >=
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	208
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	209 Then enter the value to filter and specify the column to apply that option.
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	210 If a row contains a value that correspond to your settings, it will be filtered.
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a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	212 -----
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	213
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	214 Filter by a range of values
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	215
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	216 You can also set a range of values to filter your file.
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	217 In opposition to value filter, rows with values inside of the defined range are kept.
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a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	219 Rows with values outside of the defined range will be filtered.
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a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	221 -----
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	222
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	223 AND/OR operator
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	224
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	225 Since you can add as many filters as you want, you can choose how filters apply on your data.
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a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	227 AND or OR operator option works on all filters :
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	228
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	229 - OR : only one filter to be satisfied to remove one row
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	230 - AND : all filters must be satisfied to remove one row
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	231
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	232 -----
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	233
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	234 Sort the results files
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	235
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	236 You can sort the result file if you wish, it can help you to check results.
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a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	238 In order to do so : enter the column to be used, all columns will be sorted according to the one filled in.
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a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	240 Rows stay intact, just in different order like excel.
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	241 You can also choose ascending or descending order, by default ascending order is set.
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a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	243 -----
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	244
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	245 Output
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	246
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	247 The tool will produce 2 output files.
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	248
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	249 * A text file containing the resulting filtered input file.
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	250
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	251 * A text file containing the rows removed from the input file.
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a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	253 -----
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	254
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	255 .. class:: infomark
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	256
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	257 Authors
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	258
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	259 T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	261 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	262
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	263 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	264
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	265 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	267 ]]></help>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	268 <citations>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	269 </citations>
a55e8b137c6b planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty proteore parents: diff changeset	270 </tool>

Mercurial > repos > proteore > proteore_filter_keywords_values

annotate filter_kw_val.xml @ 1:cb9555653b09 draft