Mercurial > repos > czouaoui > circoletto

changeset 5:f30bc224bb3a draft

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Deleted selected files
author czouaoui
date Tue, 13 Mar 2018 10:05:00 -0400
parents d0c745cde3f9
children 0a8b63ae836a
files circoletto.xml
diffstat 1 files changed, 0 insertions(+), 109 deletions(-) [+]
line wrap: on
line diff
--- a/circoletto.xml	Tue Mar 13 09:16:00 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,109 +0,0 @@
-<tool id="circoletto" name="Circoletto" version="0.1.0">
-    <requirements>
-	<requirement type="package" version="0.20">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>