Mercurial > repos > czouaoui > circoletto
changeset 6:0a8b63ae836a draft
Uploaded
author | czouaoui |
---|---|
date | Tue, 13 Mar 2018 10:06:02 -0400 |
parents | f30bc224bb3a |
children | 99e2897b4ad0 |
files | circoletto.xml |
diffstat | 1 files changed, 111 insertions(+), 0 deletions(-) [+] |
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--- /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>