Mercurial > repos > czouaoui > circoletto
changeset 3:97904606f60e draft
Deleted selected files
author | czouaoui |
---|---|
date | Tue, 13 Mar 2018 09:15:34 -0400 |
parents | 7059f2d7348c |
children | d0c745cde3f9 |
files | circoletto.xml |
diffstat | 1 files changed, 0 insertions(+), 111 deletions(-) [+] |
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--- a/circoletto.xml Tue Mar 13 06:47:23 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,111 +0,0 @@ -<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>