diff scaffremodler/1_create_conf.xml @ 0:66885fa414c8 draft default tip

Uploaded

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+++ b/scaffremodler/1_create_conf.xml	Mon Nov 14 08:31:23 2016 -0500
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+<tool id="1_create_conf" name="1_create_conf" version="0.1"> 
+    <description> : Create configuration file and chromosome tab file for Scaffremodler</description>  
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command>
+		source $__tool_directory__/include_scaffremodler.sh ;
+        python $__tool_directory__/1_create_conf.py
+		--tool $tool
+        #if str($reference_genome.source) == "history":
+            --ref $reference_genome.own_file  
+        #else:
+            --ref $reference_genome.genome.fields.path
+        #end if 
+		--q1 $q1
+		--q2 $q2
+		--orient $orient
+		--qual $qual
+		--mini $mini
+		--maxi $maxi
+		--index $index
+		--rmindex $rmindex
+		--mini_dis $mini_dis
+		--mult_max_cov $mult_max_cov
+		--mult_min_cov $mult_min_cov
+		--min_zone $min_zone
+		--min_gap $min_gap
+		--thread $thread
+		--msd $msd
+		--max_dist_merge $max_dist_merge
+		--YiS $YiS
+		--MiS $MiS
+		--YiC $YiC
+		--MiC $MiC
+		--min_score $min_score
+		--ploid $ploid
+		--restimate $restimate 
+		--output $config_file
+		--chr $chromosome_information
+		
+    </command>
+    <inputs>
+		<param name="tool" type="select" label="Mapping tool">
+			<option selected="true" value="bowtie2_single">bowtie2_single</option>
+			<option value="bowtie">bowtie</option>
+			<option value="bowtie2">bowtie2</option>
+			<option value="bwa">bwa</option>
+			<option value="bwa_mem">bwa_mem</option>
+		</param>
+		
+        <conditional name="reference_genome">
+        	<param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
+            	<option value="indexed">Use a built-in genome index</option>
+            	<option value="history">Use a genome from the history and build index</option>
+          	</param>
+          	<when value="indexed">
+            	<param name="genome" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the South Green team">
+					
+					<options from_data_table="scaffremodler">
+						<filter type="sort_by" column="1"/>
+						<validator type="no_options" message="No indexes are available for the selected input dataset"/>
+					</options> 
+            	</param>
+          	</when>
+          	<when value="history">
+            	<param name="own_file" type="data" format="fasta"  label="Select reference genome" />
+          	</when>
+        </conditional>		 
+		<param name="q1" type="data" format="fastq,fastqsanger" label="Mate1 fastq file" />
+		<param name="q2" type="data" format="fastq,fastqsanger" label="Mate2 fastq file" />
+		<param name="orient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand">
+			<option value="rf">RF</option>
+			<option value="fr">FR</option>
+		</param>
+		<param name="qual" type="select" label="Fastq file quality encoding 33 or 64">
+			<option selected="true" value="33">33</option>
+			<option value="64">64</option>
+		</param>
+    	<param name="mini" type="integer" value="2500" label="minimum good fragment length" />
+    	<param name="maxi" type="integer" value="7500" label="maximum good fragment length" />
+		<param name="index" type="select" label="Create index if reference not indexed">
+			<option selected="true" value="y">y</option>
+			<option value="n">n</option>
+		</param>
+		<param name="rmindex" type="select" label="Remove index">
+			<option selected="true" value="y">y</option>
+			<option value="n">n</option>
+		</param>
+		<param name="mini_dis" type="integer" value="10000" label="Minimal distance between mate to keep discordant mate (should be higher than 2 fold expected insert)" />
+		<param name="mult_max_cov" type="float" value="10" label="Multiplicator of median coverage for maximal median coverage to keep a zone" />
+		<param name="mult_min_cov" type="float" value="0.25" label="Multiplicator of median coverage for maximal median coverage to keep a zone" />
+		<param name="min_zone" type="integer" value="500" label="Minimal number of covered sites in a zone to be considered" />
+		<param name="min_gap" type="integer" value="300" label="Maximal number of contiguous uncovered sites in a zone to be considered as a single zone" />
+		<param name="thread" type="integer" value="1" label="Thread number used for mapping" />
+		<param name="msd" type="float" value="3" label="Multiplicator of standard deviation for discordant zone identification" />
+		<param name="max_dist_merge" type="float" value="1000" label="Maximal distance between two discordant zone to merge" />
+		<param name="YiS" type="float" value="0" label="Y-intercept of the linear function for zone size that will give the first component of product giving the score" />
+		<param name="MiS" type="float" value="0.5" label="Multiplicator of median insert size for calculating minimal zone size for which the first component of product giving the score will be maximal" />
+		<param name="YiC" type="float" value="0" label="Y-intercept of the linear function for coverage that will give the second component of product giving the score" />
+		<param name="MiC" type="float" value="0.25" label="Multiplicator of median coverage for calculating  minimal zone coverage for which the second component of product giving the score will be maximal" />
+		<param name="min_score" type="integer" value="70" label="minimal score for a discordant zone to be identified as passed (0 to 100)" />
+		<param name="ploid" type="float" value="0.66" label="Multiplicator for coverage variation detection in SV identification (ex : If homozygous duplication expected in diploid: expected = coverage + coverage*1; if heterozygous duplication expected in diploid => expected = coverage + coverage*0.5). Choose a value lower than the expected one" />
+		<param name="restimate" type="select" label="Re-estimate --mini and --maxi parameters">
+			<option selected="true" value="y">y</option>
+			<option value="n">n</option>
+		</param>  
+    </inputs>
+    <outputs>
+        <data format="txt" name="config_file" label="${tool.name} : Configuration file" />
+        <data format="data" name="chromosome_information" label="${tool.name} : Chromosome information" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="q1" value="reads_mate1_SV.fq"/>
+            <param name="q2" value="reads_mate2_SV.fq"/>
+			<param name="orient" value="rf"/>
+			<param name="index" value="y"/>
+			<param name="rmindex" value="y"/>
+            <param name="source" value="history" />
+            <param name="own_file" value="Ref_for_SV_detection.fasta" />
+            <output name="config_file" file="config_file.txt" compare="sim_size"/>  
+            <output name="chromosome_information" file="chromosome_information.txt"/> 
+        </test>
+    </tests>
+    <help>
+    
+**Overview**
+
+This program generate a configuration file that will be used by all other programs that begin with a number.
+
+-----
+
+.. class:: infomark
+
+**Galaxy integration** Martin Guillaume (CIRAD), Droc Gaetan (CIRAD).
+
+.. class:: infomark
+
+**Support** For any questions about Galaxy integration, please send an e-mail to [e-mail]
+
+.. class:: infomark
+
+**Program encapsulated in Galaxy by South Green**
+
+	</help>
+	<citations>
+        <citation type="doi">10.1186/s12864-016-2579-4</citation> 
+    </citations>
+</tool> 
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