view circoletto.xml @ 4:d0c745cde3f9 draft

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<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>