--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_kw_val.xml	Wed Sep 19 05:01:15 2018 -0400
@@ -0,0 +1,271 @@
+<tool id="MQoutputfilter" name="Filter by keywords or numerical value" version="2018.08.22">
+    <description></description>
+    <requirements>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        python $__tool_directory__/filter_kw_val.py
+        -i "$input1,$header"
+        -o "$output1"
+        --filtered_file "$filtered_file"
+        --operator "$operator"
+
+        ## Keywords
+        #for $key in $keyword
+            #if $key.k.kw != "None"
+                #if $key.k.kw == "text"
+                    --kw "$key.k.txt" "$key.ncol" "$key.match"
+                #else if $key.k.kw == "file"
+                    --kw_file "$key.k.file" "$key.ncol" "$key.match"
+                #end if
+            #end if
+        #end for
+
+        ## value to filter
+        #for $val in $value
+            #if $val.v.val != "None"
+                --value
+                #if $val.v.val == "Equal"
+                    $val.v.equal "$val.ncol" "="
+                #else if $val.v.val == "Higher"
+                    $val.v.higher "$val.ncol" ">"
+                #else if $val.v.val == "Equal or higher"
+                    $val.v.equal_higher "$val.ncol" ">="
+                #else if $val.v.val == "Lower"
+                    $val.v.lower "$val.ncol" "<"
+                #else if $val.v.val == "Equal or lower"
+                    $val.v.equal_lower "$val.ncol" "<="
+                #else 
+                    $val.v.different "$val.ncol" "!="
+                #end if
+            #end if
+        #end for
+
+        ##range of values to keep
+        #for $vr in $values_range
+            #if vr 
+                --values_range $vr.bottom_value $vr.top_value $vr.ncol $vr.inclusive
+            #end if
+        #end for
+
+        #if $sort_column != ""
+            --sort_col "$sort_column,$reversed_sort"
+        #end if
+
+    ]]></command>
+    <inputs>
+        <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" />
+        <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
+        <param name="operator" type="select" label="Please select an operator for your filters" help="OR : only one filter must be satisfied to filter a row, AND : all your filters must be satisfied to filter a row" >
+            <option value="OR" selected="True">OR</option>
+            <option value="AND">AND</option>
+        </param>
+        <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." />
+        <param name="reversed_sort" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Sort in descending order ?"/>        
+        <repeat name="keyword" title="Filter by keywords" >
+            <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' />
+            <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' />
+            <conditional name="k" >
+                <param argument="--kw" type="select" label="Filter by keyword" >
+                    <option value="None" selected="True">---</option>
+                    <option value="text">Enter keywords (copy/paste)</option>
+                    <option value="file">Choose a file containing keywords</option>
+                </param>
+                <when value="None" />
+                <when value="text" >
+                    <param name="txt" type="text" label="Copy/paste keywords to be filtered out" help='Keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175' >
+                        <sanitizer>
+                        <valid initial="string.printable">
+                            <remove value="&apos;"/>
+                        </valid>
+                        <mapping initial="none">
+                            <add source="&apos;" target="__sq__"/>
+                        </mapping>
+                        </sanitizer>
+                    </param>
+                </when>
+                <when value="file" >
+                    <param name="file" type="data" format="txt,tabular" label="Choose a file containing keywords" />
+                </when>
+            </conditional>
+        </repeat>
+        <repeat name="value" title="Filter by value" >
+            <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' />
+            <conditional name="v" >
+                <param argument="--val" type="select" label="Filter by value" >
+                    <option value="None">---</option>
+                    <option value="Equal">=</option>
+                    <option value="Higher">&gt;</option>
+                    <option value="Equal or higher">&gt;=</option>
+                    <option value="Lower">&lt;</option>
+                    <option value="Equal or lower">&lt;=</option>
+                    <option value="Different">!=</option>
+                </param>
+                <when value="None" >
+                </when>
+                <when value="Equal" >
+                    <param name="equal" type="float" value="" label="Value" />
+                </when>
+                <when value="Higher" >
+                    <param type="float" name="higher" value="" label="Value" />
+                </when>
+                <when value="Equal or higher" >
+                    <param type="float" name="equal_higher" value="" label="Value" />
+                </when>
+                <when value="Lower" >
+                    <param type="float" name="lower" value="" label="Value" />
+                </when>
+                <when value="Equal or lower" >
+                    <param type="float" name="equal_lower" value="" label="Value" />
+                </when>
+                <when value="Different">
+                    <param type="float" name="different" value="" label="Value"/>
+                </when>
+            </conditional>
+        </repeat>
+        <repeat name="values_range" title="Filter by range of values">
+            <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' />
+            <param name="bottom_value" type="float" value="" label="Please enter the bottom value" />
+            <param name="top_value" type="float" value="" label="Please enter the top value" />
+            <param name="inclusive" type="boolean" label="inclusive range ?" checked="false" truevalue="true" falsevalue="false" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="output1" format="tabular" label="${tool.name} on ${input1.name}" />
+        <data name="filtered_file" format="tabular" label="${tool.name} on ${input1.name} - Filtered lines" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="Lacombe_et_al_2017_OK.txt" />
+            <param name="header" value="true" />
+            <param name="operator" value="OR"/>
+            <param name="sort_column" value="c1"/>
+            <param name="reversed_sort" value="false"/>
+            <repeat name="keyword">
+                <param name="ncol" value="c1" />
+                <param name="match" value="True" />
+                <conditional name="k">
+                    <param name="kw" value="text" />
+                    <param name="txt" value="P04264;P35908;P13645;Q5D862;Q5T749;Q8IW75;P81605;P22531;P59666;P78386" />
+                </conditional>
+            </repeat>
+            <repeat name="value">
+                <param name="ncol" value="c3"/>
+                <conditional name="v">
+                    <param name="val" value="Higher"/>
+                    <param name="higher" value="20" />
+                </conditional>
+            </repeat>
+            <output name="output1" file="output.csv" />
+            <output name="filtered_file" file="filtered_output.csv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output).
+
+**Filter by keyword(s)**
+
+Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords.
+
+- If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175
+
+- If you choose to upload a file in a text format in which each line is a keyword, for example:
+
+REV
+
+TRYP_PIG
+
+ALDOA_RABBIT
+
+**The line that contains these keywords will be eliminated from input file.**
+
+**Keywords search can be applied by performing either exact match or partial one by using the following option**
+
+- If you choose **Yes**, only the fields that contains exactly the same content will be removed.
+
+- If you choose **No**, all the fields containing the keyword will be removed.
+
+For example:
+
+**Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed.
+
+**No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so  on) are removed.
+
+-----
+
+**Filter by values**
+
+You can filter your data by a column of numerical values.
+Enter the column to be use and select one operator in the list :
+
+- =
+- !=
+- <
+- <=
+- >
+- >=
+
+Then enter the value to filter and specify the column to apply that option.
+If a row contains a value that correspond to your settings, it will be filtered.
+
+-----
+
+**Filter by a range of values**
+
+You can also set a range of values to filter your file.
+In opposition to value filter, rows with values inside of the defined range are kept.
+
+Rows with values outside of the defined range will be filtered.
+
+-----
+
+**AND/OR operator**
+
+Since you can add as many filters as you want, you can choose how filters apply on your data.
+
+AND or OR operator option works on all filters :
+
+- OR : only one filter to be satisfied to remove one row
+- AND : all filters must be satisfied to remove one row
+
+-----
+
+**Sort the results files**
+
+You can sort the result file if you wish, it can help you to check results. 
+
+In order to do so : enter the column to be used, all columns will be sorted according to the one filled in.
+
+Rows stay intact, just in different order like excel.
+You can also choose ascending or descending order, by default ascending order is set.
+
+-----
+
+**Output**
+
+The tool will produce 2 output files.
+
+* A text file containing the resulting filtered input file.
+
+* A text file containing the rows removed from the input file.
+
+-----
+
+.. class:: infomark
+
+**Authors**
+
+T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+
+Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
+
+This work has been partially funded through the French National Agency for Research (ANR) IFB project.
+
+Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
+
+    ]]></help>
+    <citations>
+    </citations>
+</tool>