# HG changeset patch
# User czouaoui
# Date 1520949962 14400
# Node ID 0a8b63ae836a23c1ae8bab5d2f1f3f0375d65e1e
# Parent  f30bc224bb3a098b7c047b26132f7e57e2ecf3ee
Uploaded

diff -r f30bc224bb3a -r 0a8b63ae836a circoletto.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/circoletto.xml	Tue Mar 13 10:06:02 2018 -0400
@@ -0,0 +1,111 @@
+<tool id="circoletto" name="Circoletto" version="0.1.0">
+    <requirements>
+	<requirement type="package" version="0.69.5">circos</requirement>
+	<requirement type="package" version="1.6.924">perl-bioperl</requirement>
+	<requirement type="package" version="0.22">circostools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        perl $__tool_directory__/circoletto.pl -bl $input --out_name circoletto
+	#if $settings.advanced == "advanced"	
+	   #if $settings.link_colors_by.select_link_colors_by == "score"
+	       --score2colour bit
+	   #end if
+	   #if $settings.link_colors_by.select_link_colors_by == "eval"
+	       --score2colour eval
+	   #end if
+	   #if $settings.link_colors_by.select_link_colors_by == "identite"
+	       --score2colour id
+	   #end if
+	   #if $settings.best_hit.select_best_hit == "yes"
+	       --best_hit
+	   #end if
+	   #if $settings.query_order.select_query_order == "invert"
+	       --reverse_qorder
+	   #end if
+	   #if $settings.db_order.select_db_order == "invert"
+	       --reverse_dorder
+	   #end if
+	   #if $settings.color_range.select_color_range == "min"
+	       --scoreratio2colour max
+	   #end if
+	   #if $settings.color_range.select_color_range == "sup"
+	       --scoreratio2colour minmax
+	   #end if
+	   #if $settings.select_links_allowed.value
+	       #set links_allowed = '(' + '|'.join( [ str( $link_type ) for $link_type in $settings.select_links_allowed.value ] ) + ')'
+	       --ribocolours2allow "${links_allowed}"
+	   #end if
+	#end if
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" label="Résultat BLAST"/>
+        <conditional name="settings">
+            <param name="advanced" type="select" label="Paramètres avancés">
+                <option value="simple" selected="true">Non, utiliser les paramètres par défaut.</option>
+                <option value="advanced">Oui, voir la liste des paramètres.</option>
+            </param>
+            <when value="simple">
+            </when>
+            <when value="advanced">
+		<conditional name="link_colors_by">
+		    <param name="select_link_colors_by" type="select" label="Coloration des alignements en fonction">
+		        <option value="score" selected="true">Du bit score</option>
+		        <option value="eval">De l'e-value</option>
+			<option value="identite">Du % d'identité</option>
+		    </param>
+		</conditional>
+	    	<param name="select_links_allowed" type="select" label="Séléction des alignements à afficher" multiple="true">
+		        <option value="blue" selected="true">Bleu (0 - 25%)</option>
+		        <option value="green" selected="true">Vert (25 - 50%)</option>
+			<option value="orange" selected="true">Orange (50 - 75%)</option>
+			<option value="red" selected="true">Rouge (75 - 100%)</option>
+	    	</param>
+		<conditional name="best_hit">
+		    <param name="select_best_hit" type="select" label="Afficher seulement le meilleur alignement pour chaque séquence interrogée">
+		        <option value="no" selected="true">Non</option>
+		        <option value="yes">Oui</option>
+		    </param>
+		</conditional>
+		<conditional name="query_order">
+		    <param name="select_query_order" type="select" label="Ordre des séquences interrogées">
+		        <option value="default" selected="true">Par défaut</option>
+		        <option value="invert">Inversé</option>
+		    </param>
+		</conditional>
+		<conditional name="db_order">
+		    <param name="select_db_order" type="select" label="Ordre des séquences de références">
+		        <option value="default" selected="true">Par défaut</option>
+		        <option value="invert">Inversé</option>
+		    </param>
+		</conditional>
+		<conditional name="color_range">
+		    <param name="select_color_range" type="select" label="Gamme de couleurs">
+		        <option value="min" selected="true">Par défaut</option>
+		        <option value="sup">Supérieure</option>
+		    </param>
+		</conditional>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name= "output" format="png" label="${tool.name} -  ${input.name}" from_work_dir="circoletto.png"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="blast_170144"/>
+            <output name="output" file="circoletto.png"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Cet outil utilise un fichier comportant un résultat de BLAST afin de visualiser, via Circos, les similarités entre les séquences interrogées et les séquences de références.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubseqtk,
+  title = {Circoletto},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/infspiredBAT/Circoletto},
+}</citation>
+    </citations>
+</tool>