--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_sequence_file.xml	Wed Jan 27 02:50:51 2016 -0500
@@ -0,0 +1,296 @@
+<tool id="extract_sequence_file" name="Extract" version="0.1.0">
+
+	<description>from sequence file</description>
+
+    <macros>
+        <xml name="fasta_option">
+            <option value="id">Identifiant</option>
+            <option value="length">Length</option>
+            <option value="description">Description</option>
+        </xml>
+        <xml name="fastq_option">
+            <option value="id">Identifiant</option>
+            <option value="length">Length</option>
+            <option value="description">Description</option>
+        </xml>
+        <xml name="test_constrain_extraction">
+            <param name='constrained_extraction' type='boolean' checked="false" 
+                truevalue='true' falsevalue='false' label="Constrain extraction?" help=""/>
+        </xml>
+        <xml name="constrain_string">
+            <conditional name="constraint_type">
+                <param name="type" type="select" display="radio" label="Type of 
+                    constraint" help="">
+                    <option value="equal">Equal a value</option>
+                    <option value="in">In a list</option>
+                    <option value="not_in">Not in a list</option>
+                </param>
+                <when value="equal">
+                    <param name="value" type="text" size="200" label="Equal to" 
+                        help=""/>
+                    <validator type="empty_field" message="Give a value"/>
+                </when>
+                <when value="in">
+                    <param format="txt" name="value" type="data" label="List of 
+                        constraint" help="Text file with a value per line and 
+                        nothing else"/>
+                    <validator type="unspecified_build" message="Select a file"/>
+                </when>
+                <when value="not_in">
+                    <param format="txt" name="value" type="data" label="List of 
+                        constraint" help="Text file with a value per line and 
+                        nothing else"/>
+                    <validator type="unspecified_build" message="Select a file"/>
+                </when>
+            </conditional>
+        </xml>
+        <xml name="constrain_number">
+            <param name="type" type="select" label="Type of constraint" help="">
+                <option value="equal">Equal to </option>
+                <option value="lower">Lower than </option>
+                <option value="strictly_lower">Strictly lower than </option>
+                <option value="greater">Greater than </option>
+                <option value="strictly_greater">Strictly greater than </option>
+            </param>
+        </xml>
+        <xml name="constraint_definitions">
+            <conditional name="constraints">
+                <expand macro="test_constrain_extraction" />
+                <when value="true">
+                    <repeat name="constraint_definition" title="Constraints on 
+                        sequences" min="1">
+                        <conditional name="constrained_information">
+                            <param name="info_to_constrain" type="select" 
+                                label="Information to constrain" help="">
+                                <option value="id">Identifiant</option>
+                                <option value="length">Length</option>
+                            </param>
+                            <when value="id">
+                                <expand macro="constrain_string" />
+                            </when>  
+                            <when value="length">
+                                <repeat name="constraint_definition" title="Constraint 
+                                    on sequence length" min="1">
+                                    <expand macro="constrain_number" />
+                                    <param name="value" type="integer" min="0" 
+                                        max="3000" value="100" label="Value" help=""/>
+                                </repeat>
+                            </when>  
+                        </conditional>
+                    </repeat>
+                </when>
+                <when value="false" />
+            </conditional>
+        </xml>
+    </macros>
+
+	<requirements>
+  	</requirements>
+
+    <stdio>
+    </stdio>
+
+    <version_command><![CDATA[python -version]]></version_command>
+
+  	<!--<command>-->
+    <command><![CDATA[
+  		python $__tool_directory__/extract_sequence_file.py 
+      		--input=$sequence_file_format.sequence_file
+
+            --custom_extraction_type=$sequence_file_format.extraction.specific_extraction
+            #if $sequence_file_format.extraction.specific_extraction :
+                --to_extract="{$sequence_file_format.extraction.to_extract}"
+                --output_information=$information_file
+            #else if $sequence_file_format.format=="fastq":
+                --split=$sequence_file_format.extraction.split.split_test
+                #if $sequence_file_format.extraction.split.split_test :
+                    --quality_format=$sequence_file_format.extraction.split.quality_format
+                    --output_sequence=$fasta_sequence_file_from_fastq
+                    --output_quality=$quality_file
+                #else:
+                    --output_sequence=$fastq_sequence_file
+                #end if
+            #else:
+                --output_sequence=$fasta_sequence_file
+            #end if
+                
+    		#if $constraints.constrained_extraction :
+                #for $i, $constrain in enumerate( $constraints.constraint_definition )
+                	#set info_to_constrain=$constrain.constrained_information['info_to_constrain']             
+                    #if $info_to_constrain in ("id"):
+                    	--constraint="$info_to_constrain:
+                    	${constrain.constrained_information.constraint_type.type}:
+                    	${constrain.constrained_information.constraint_type.value}"
+                    #else:
+                    	#for $j, $sub_constrain in enumerate( $constrain.constrained_information.constraint_definition )
+                    		--constraint="$info_to_constrain:
+                    		${sub_constrain.type}:
+                    		${sub_constrain.value}"
+                        #end for
+                    #end if
+                #end for
+            #end if
+
+            --report $report_filepath
+            --format=$sequence_file_format.format
+        ]]>
+  	</command>
+
+  	<inputs>
+        <conditional name="sequence_file_format">
+        	<param name="format" type="select" display="radio" 
+                label="Format of the sequence file" help="">
+	            <option value="fasta">Fasta</option>
+                <option value="fastq">FastQ</option>
+	        </param>
+            <when value="fastq">
+                <param name="sequence_file" type="data" format="fastq" 
+                    label="Sequence file" help=""/>
+                <conditional name="extraction">
+                    <param name='specific_extraction' type='boolean' 
+                        checked="false" truevalue='true' falsevalue='false'
+                        label="Extract specific information?" 
+                        help="If no is selected, a sequence file is generated. 
+                        If yes, a text file containing the wanted information is 
+                        generated"/>
+                    <when value="true">
+                        <param name="to_extract" type="select" display="checkboxes" 
+                            multiple="true" label="Information to extract" help="">
+                            <expand macro="fasta_option" />
+                            <validator type="no_options" message="Select at least 
+                                one information to extract"/>
+                        </param>
+                    </when>
+                    <when value="false">
+                        <conditional name="split">
+                            <param name='split_test' type='boolean' checked="false"
+                                truevalue='true' falsevalue='false' label="Split 
+                                file into sequence and quality files?" help="If 
+                                yes is selected, a fasta and a quality file are 
+                                generated. If no, a fastq file is generated"/>
+                            <when value="true">
+                                <param name="quality_format" type="select" 
+                                    display="radio" label="Coding of quality 
+                                    scores?" help="">
+                                    <option value="sanger" selected="true">Sanger (Phred+33)</option>
+                                    <option value="solexa">Solexa (Solexa+64) </option>
+                                    <option value="illumina_1_3">Illumina 1.3+ (Phred+64) </option>
+                                    <option value="illumina_1_5">Illumina 1.5+ (Phred+64) </option>
+                                    <option value="illumina_1_8">Illumina 1.8+ (Phred+33) </option>
+                                </param>
+                            </when>
+                            <when value="false" />
+                        </conditional> 
+                    </when>
+                </conditional> 
+            </when>
+            <when value="fasta">
+                <param name="sequence_file" type="data" format="fasta" 
+                    label="Sequence file" help=""/>
+                <conditional name="extraction">
+                    <param name='specific_extraction' type='boolean' checked="false" 
+                        truevalue='true' falsevalue='false' label="Extract specific 
+                        information?" help="If no is selected, a sequence file is 
+                        generated. If yes, a text file containing the wanted 
+                        information is generated"/>
+                    <when value="true">
+                        <param name="to_extract" type="select" display="checkboxes" 
+                            multiple="true" label="Information to extract" help="">
+                            <expand macro="fasta_option" />
+                            <validator type="no_options" message="Select at least 
+                                one information to extract"/>
+                        </param>
+                    </when>
+                    <when value="false" />
+                </conditional> 
+            </when>
+        </conditional>
+        
+        <expand macro="constraint_definitions" />
+  	</inputs>
+
+  	<outputs>
+        <data format="txt" name="information_file" 
+            label="${tool.name} on ${on_string}: Information">
+            <filter>((sequence_file_format['extraction']['specific_extraction']))</filter>
+        </data>
+
+        <data format="fasta" name="fasta_sequence_file"
+            label="${tool.name} on ${on_string}: Extracted sequences" >
+            <filter>((sequence_file_format['format'] == 'fasta' and 
+                not sequence_file_format['extraction']['specific_extraction']))</filter>
+        </data>
+
+        <data format="fastq" name="fastq_sequence_file"
+            label="${tool.name} on ${on_string}: Extracted sequences">
+            <filter>((sequence_file_format['format'] == 'fastq' and 
+                not sequence_file_format['extraction']['specific_extraction'] and
+                not sequence_file_format['extraction']['split']['split_test']))</filter>
+        </data>
+
+        <data format="qual" name="quality_file" 
+            label="${tool.name} on ${on_string}: Extracted quality">
+            <filter>((sequence_file_format['format'] == 'fastq' and 
+                not sequence_file_format['extraction']['specific_extraction'] and
+                sequence_file_format['extraction']['split']['split_test']))</filter>
+        </data>
+
+        <data format="fasta" name="fasta_sequence_file_from_fastq"
+            label="${tool.name} on ${on_string}: Extracted sequences">
+            <filter>((sequence_file_format['format'] == 'fastq' and 
+                not sequence_file_format['extraction']['specific_extraction'] and
+                sequence_file_format['extraction']['split']['split_test']))</filter>
+        </data>
+
+        <data format="txt" name="report_filepath" 
+            label="${tool.name} on ${on_string}: Report"/>
+  	</outputs>
+
+  	<tests>
+  		<test>
+  			<param name="sequence_file_format.sequence_file" 
+                value="read_write_fasta_file/input_sequence_file.fasta"/>
+  			<param name="sequence_file_format.extraction.specific_extraction" 
+                value="false"/>
+            <param name="$sequence_file_format.format" value="fasta" />
+  			<output name="fasta_sequence_file" 
+                file="read_write_fasta_file/input_sequence_file.fasta"/>
+  			<output name="report_filepath" 
+                file="read_write_fasta_file/expected_output_report.txt"/>
+  		</test>
+  	</tests>
+
+  	<help><![CDATA[
+
+**What it does**
+
+This tool extracts information from sequence files. 
+
+Some constraints could be added to extraction. For example, you choose 
+to extract only sequences for which the length is greater than 30 bp.
+
+More information on `ASaiM documentation <http://asaim.readthedocs.org/>`_...
+
+-----
+
+**Input**
+
+The input is one file in fasta or fastq.
+
+-----
+
+**Outputs**
+
+The tool generates different outputs given the choosen parameters:
+
+    - a sequence file
+    - a text file
+    - a sequence file and a quality file
+
+]]>
+  	</help>
+
+    <citations>
+    </citations>
+</tool>
+