--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_kw_val.xml	Sun Nov 26 18:36:43 2017 -0500
@@ -0,0 +1,202 @@
+<tool id="MQoutputfilter" name="Filter out keywords and/or numerical values" version="0.1.0">
+    <description>Filter a file by keywords or values</description>
+    <requirements>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        python $__tool_directory__/filter_kw_val.py 
+        -i "$input1,$header" 
+        -o "$output1"
+        --trash_file "$trash_file"
+
+        ## Keywords
+        #for $i, $key in enumerate($keyword)
+            #if $key.k.kw != "None"
+                #if $key.k.kw == "text"
+                    --kw "$key.k.txt" "$key.k.ncol" "$key.match"
+                #else if $key.k.kw == "file"
+                    --kw_file "$key.k.file" "$key.k.ncol" "$key.match"
+                #end if
+            #end if
+        #end for
+        
+        ## Number of proteins
+        #for $i, $val in enumerate($value)
+            #if $val.v.val != "None"
+                --value
+                #if $val.v.val == "Equal"
+                    $val.v.equal "$value.ncol" "="
+                #else if $val.v.val == "Higher"
+                    $val.v.higher "$val.v.ncol" ">"
+                #else if $val.v.val == "Equal or higher"
+                    $val.v.equal_higher "$val.v.ncol" ">="
+                #else if $val.v.val == "Lower"
+                    $val.v.lower "$val.v.ncol" "<"
+                #else
+                    $val.v.equal_lower "$val.v.ncol" "<="
+                #end if
+            #end if
+        #end for
+       
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="txt,tabular" label="Input file" help="Input file is a tab-delimited file containing proteomics results (e.g. output file from MaxQuant or Proline softwares" />
+        <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
+        <repeat name="keyword" title="Filter by keywords" >
+            <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 detail' />
+            <conditional name="k" >
+                <param argument="--kw" type="select" label="Filter by keyword" >
+                    <option value="None" selected="True">---</option>
+                    <option value="text">Enter keywords</option>
+                    <option value="file">Choose a file containing keywords</option>
+                </param>
+                <when value="None" />
+                <when value="text" >
+                    <param name="txt" type="text" label="Enter keywords or a file containing keywords to be removed" >
+                        <sanitizer>
+                        <valid initial="string.printable">
+                            <remove value="&apos;"/>
+                        </valid>
+                        <mapping initial="none">
+                            <add source="&apos;" target="__sq__"/>
+                        </mapping>
+                        </sanitizer>
+                    </param>
+                    <param name="ncol" type="text" value="c1" label="Please specify the column where you would like to apply this filter" help='For example, fill in "c1" if you want to filter the first column' />
+                </when>
+                <when value="file" >
+                    <param name="file" type="data" format="txt,tabular" label="Choose a file containing keywords" />
+                    <param name="ncol" type="text" value="c1" label="Please specify the column on which to apply this filter" help='For example, fill in "c1" if the keyword you want to filter out is expected in the first column' />
+                </when>
+            </conditional>
+        </repeat>
+        
+        <repeat name="value" title="Filter by value" >
+            <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>
+                </param>
+                <when value="None" >
+                </when>
+                <when value="Equal" >
+                    <param name="equal" type="float" value="" label="Value" />
+                    <param name="ncol" type="text" value="c1" label="Please specify the column where you would like to apply this filter" help='For example, fill in "c1" if you want to filter the first column' />
+                </when>
+                <when value="Higher" >
+                    <param type="float" name="higher" value="" label="Value" />
+                    <param name="ncol" type="text" value="c1" label="Please specify the column where you would like to apply this filter" help='For example, fill in "c1" if you want to filter the first column' />
+                </when>
+                <when value="Equal or higher" >
+                    <param type="float" name="equal_higher" value="" label="Value" />
+                    <param name="ncol" type="text" value="c1" label="Please specify the column where you would like to apply this filter" help='For example, fill in "c1" if you want to filter the first column' />
+                </when>
+                <when value="Lower" >
+                    <param type="float" name="lower" value="" label="Value" />
+                    <param name="ncol" type="text" value="c1" label="Please specify the column where you would like to apply this filter" help='For example, fill in "c1" if you want to filter the first column' />
+                </when>
+                <when value="Equal or lower" >
+                    <param type="float" name="equal_lower" value="" label="Value" />
+                    <param name="ncol" type="text" value="c1" label="Please specify the column where you would like to apply this filter" help='For example, fill in "c1" if you want to filter the first column' />
+                </when>
+            </conditional>
+        </repeat>
+   
+    </inputs>
+    <outputs>
+        <data name="output1" format="tabular" label="${tool.name} on ${input1.name}" />
+        <data name="trash_file" format="tabular" label="Removed proteins from input file" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="UnipIDs.txt" />
+            <param name="header" value="false" />
+            <repeat name="keyword">
+                <param name="match" value="false" />
+                <conditional name="k">
+                    <param name="kw" value="text" />
+                    <param name="txt" value="A" />
+                    <param name="ncol" value="c3" />
+                </conditional>
+            </repeat>
+            <repeat name="value">
+                <conditional name="v">
+                    <param name="val" value="Equal or higher"/>
+                    <param name="equal_higher" value="1.0" />
+                    <param name="ncol" value="c2" />
+                </conditional>
+            </repeat>
+            <output name="output1" file="filter_keywords_values_output.txt" />
+            <output name="trash_file" file="filter_keywords_values_removed.txt" />
+        </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).
+
+**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**
+
+**Filter the file by keywords**
+
+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 the file by values**
+
+You can choose to use one or more options (e.g. to filter out peptides of low intensity value, by q-value, etc.).
+
+* For each option, you can choose between "=", ">", ">=", "<" and "<=", then enter the value to filter and specify the column to apply that option.
+
+**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, 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
+
+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>