Mercurial > repos > iuc > busco

diff busco.xml @ 22:e5c372c91e46 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 8565e8283f976870104e08aa7729a1624edd6f58
author iuc
date Tue, 29 Oct 2024 14:13:47 +0000
parents 2babe6d5c561
children
line wrap: on
line diff
--- a/busco.xml	Fri Aug 30 15:19:56 2024 +0000
+++ b/busco.xml	Tue Oct 29 14:13:47 2024 +0000
@@ -1,5 +1,5 @@
-<tool id="busco" name="Busco" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
-    <description>assess genome assembly and annotation completeness</description>
+<tool id="busco" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>Assess genome assembly and annotation completeness</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -54,7 +54,6 @@
     #elif $busco_mode.use_augustus.use_augustus_selector == 'augustus':
         ${busco_mode.use_augustus.long}
         --augustus
-
         #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
             --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
         #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
@@ -84,9 +83,9 @@
 #end if
 
 
-]]>    </command>
+]]></command>
     <inputs>
-        <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." />
+        <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set."/>
         <conditional name="lineage_conditional">
             <param name="selector" type="select" label="Lineage data source">
                 <option value="download">Download lineage data</option>
@@ -95,7 +94,7 @@
             <when value="cached">
                 <param name="cached_db" label="Cached database with lineage" type="select">
                     <options from_data_table="busco_database">
-                        <validator message="No BUSCO database is available" type="no_options" />
+                        <validator message="No BUSCO database is available" type="no_options"/>
                     </options>
                 </param>
             </when>
@@ -113,7 +112,6 @@
                         <option value="augustus">Augustus</option>
                         <option value="metaeuk">Metaeuk</option>
                         <option value="miniprot" selected="true">Miniprot</option>
-
                     </param>
                     <when value="metaeuk"/>
                     <when value="miniprot"/>
@@ -124,24 +122,23 @@
                                 <option value="builtin">Use another predefined species model</option>
                                 <option value="history">Use a custom species model</option>
                             </param>
-                            <when value="no" />
+                            <when value="no"/>
                             <when value="history">
-                                <param name="augustus_model" type="data" format="augustus" label="Augustus model" />
+                                <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>
                             </when>
                             <when value="builtin">
                                 <param name="augustus_species" type="select" label="Augustus species model">
-                                    <expand macro="augustus_species" />
+                                    <expand macro="augustus_species"/>
                                 </param>
                             </when>
                         </conditional>
-                        <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms" />
+                        <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/>
                     </when>
                 </conditional>
             </when>
-            <when value="tran" />
-            <when value="prot" />
+            <when value="tran"/>
+            <when value="prot"/>
         </conditional>
-
         <conditional name="lineage">
             <param name="lineage_mode" type="select" label="Auto-detect or select lineage?" help="Let BUSCO decide the best lineage automatically, or select from known lineage">
                 <option value="auto_detect">Auto-detect</option>
@@ -156,7 +153,7 @@
             </when>
             <when value="select_lineage">
                 <param argument="--lineage_dataset" type="select" label="Lineage">
-                    <expand macro="lineages" />
+                    <expand macro="lineages"/>
                 </param>
             </when>
         </conditional>
@@ -169,8 +166,8 @@
         </param>
 
         <section name="adv" title="Advanced Options" expanded="False">
-            <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
-            <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
+            <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches."/>
+            <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
             <param argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/>
         </section>
     </inputs>
@@ -179,7 +176,7 @@
         <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
             <filter>outputs and 'short_summary' in outputs</filter>
         </data>
-        <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" />
+        <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv"/>
         <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
             <filter>outputs and 'missing' in outputs</filter>
         </data>
@@ -193,148 +190,148 @@
     
     <tests>
         <test expect_num_outputs="4">
-            <param name="input" value="genome.fa" />
+            <param name="input" value="genome.fa"/>
             <conditional name="lineage">
-                <param name="lineage_mode" value="select_lineage" />
-                <param name="lineage_dataset" value="arthropoda_odb10" />
+                <param name="lineage_mode" value="select_lineage"/>
+                <param name="lineage_dataset" value="arthropoda_odb10"/>
             </conditional>
             <conditional name="busco_mode">
-                <param name="mode" value="geno" />
+                <param name="mode" value="geno"/>
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="augustus" />
+                    <param name="use_augustus_selector" value="augustus"/>
                 </conditional>
             </conditional>
-            <param name="outputs" value="short_summary,missing,gff" />
+            <param name="outputs" value="short_summary,missing,gff"/>
             <output name="busco_sum">
                 <assert_contents>
                     <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
                     <has_text text="Gene predictor used: augustus"/>
                 </assert_contents>
             </output>
-            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
+            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
             <output name="busco_gff">
                 <assert_contents>
                     <has_n_lines n="1"/>
-                    <has_text text="##gff-version 3" />
+                    <has_text text="##gff-version 3"/>
                 </assert_contents>
             </output>
             <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
         </test>
         <test expect_num_outputs="5">
-            <param name="input" value="proteome.fa" />
+            <param name="input" value="proteome.fa"/>
             <conditional name="lineage">
-                <param name="lineage_mode" value="select_lineage" />
-                <param name="lineage_dataset" value="arthropoda_odb10" />
+                <param name="lineage_mode" value="select_lineage"/>
+                <param name="lineage_dataset" value="arthropoda_odb10"/>
             </conditional>
             <conditional name="busco_mode">
-                <param name="mode" value="prot" />
+                <param name="mode" value="prot"/>
             </conditional>
-            <param name="outputs" value="short_summary,missing,image,gff" />
+            <param name="outputs" value="short_summary,missing,image,gff"/>
             <output name="busco_sum">
                 <assert_contents>
                     <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
-                    <has_text text="BUSCO was run in mode: proteins" />
+                    <has_text text="BUSCO was run in mode: proteins"/>
                 </assert_contents>
             </output>
-            <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10" />
-            <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10" />
-            <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
+            <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10"/>
+            <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
+            <output name="summary_image" file="proteome_results/summary.png" compare="sim_size"/>
             <output name="busco_gff">
                 <assert_contents>
                     <has_n_lines n="1"/>
-                    <has_text text="##gff-version 3" />
+                    <has_text text="##gff-version 3"/>
                 </assert_contents>
             </output>
         </test>
         <test expect_num_outputs="5">
-            <param name="input" value="transcriptome.fa" />
+            <param name="input" value="transcriptome.fa"/>
             <conditional name="lineage">
-                <param name="lineage_mode" value="select_lineage" />
-                <param name="lineage_dataset" value="arthropoda_odb10" />
+                <param name="lineage_mode" value="select_lineage"/>
+                <param name="lineage_dataset" value="arthropoda_odb10"/>
             </conditional>
             <conditional name="busco_mode">
-                <param name="mode" value="tran" />
+                <param name="mode" value="tran"/>
             </conditional>
-            <param name="outputs" value="short_summary,missing,image,gff" />
+            <param name="outputs" value="short_summary,missing,image,gff"/>
             <output name="busco_sum">
                 <assert_contents>
-                    <has_text text="BUSCO was run in mode: euk_tran" />
+                    <has_text text="BUSCO was run in mode: euk_tran"/>
                 </assert_contents>
             </output>
-            <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
-            <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
-            <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
-            <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" />
+            <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6"/>
+            <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6"/>
+            <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size"/>
+            <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff"/>
         </test>
         <test expect_num_outputs="3">
-            <param name="input" value="genome.fa" />
+            <param name="input" value="genome.fa"/>
             <conditional name="lineage">
-                <param name="lineage_mode" value="select_lineage" />
-                <param name="lineage_dataset" value="arthropoda_odb10" />
+                <param name="lineage_mode" value="select_lineage"/>
+                <param name="lineage_dataset" value="arthropoda_odb10"/>
             </conditional>
             <conditional name="busco_mode">
-                <param name="mode" value="geno" />
+                <param name="mode" value="geno"/>
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="augustus" />
+                    <param name="use_augustus_selector" value="augustus"/>
                     <conditional name="aug_prediction">
-                        <param name="augustus_mode" value="builtin" />
-                        <param name="augustus_species" value="human" />
+                        <param name="augustus_mode" value="builtin"/>
+                        <param name="augustus_species" value="human"/>
                     </conditional>
                 </conditional>
             </conditional>
-            <param name="outputs" value="short_summary,gff" />
+            <param name="outputs" value="short_summary,gff"/>
             <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
                 <assert_contents>
                     <has_text text="# Gene predictor used: augustus"/>
                 </assert_contents>
             </output>
-            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
+            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
             <output name="busco_gff">
                 <assert_contents>
                     <has_n_lines n="1"/>
-                    <has_text text="##gff-version 3" />
+                    <has_text text="##gff-version 3"/>
                 </assert_contents>
             </output>
         </test>
         <test expect_num_outputs="3">
-            <param name="input" value="genome.fa" />
+            <param name="input" value="genome.fa"/>
             <conditional name="lineage">
-                <param name="lineage_mode" value="select_lineage" />
-                <param name="lineage_dataset" value="arthropoda_odb10" />
+                <param name="lineage_mode" value="select_lineage"/>
+                <param name="lineage_dataset" value="arthropoda_odb10"/>
             </conditional>
             <conditional name="busco_mode">
-                <param name="mode" value="geno" />
+                <param name="mode" value="geno"/>
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="augustus" />
+                    <param name="use_augustus_selector" value="augustus"/>
                     <conditional name="aug_prediction">
-                        <param name="augustus_mode" value="history" />
-                        <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
+                        <param name="augustus_mode" value="history"/>
+                        <param name="augustus_model" value="local.tar.gz" ftype="augustus"/>
                     </conditional>
                 </conditional>
             </conditional>
-            <param name="outputs" value="short_summary,missing" />
+            <param name="outputs" value="short_summary,missing"/>
             <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10">
                 <assert_contents>
                     <has_text text="# Gene predictor used: augustus"/>
                     <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
                 </assert_contents>
             </output>
-            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" />
-            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10" />
+            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10"/>
+            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/>
         </test>
         <test expect_num_outputs="5">
-            <param name="input" value="genome.fa" />
+            <param name="input" value="genome.fa"/>
             <conditional name="lineage">
-                <param name="lineage_mode" value="select_lineage" />
-                <param name="lineage_dataset" value="arthropoda_odb10" />
+                <param name="lineage_mode" value="select_lineage"/>
+                <param name="lineage_dataset" value="arthropoda_odb10"/>
             </conditional>
             <conditional name="busco_mode">
-                <param name="mode" value="geno" />
+                <param name="mode" value="geno"/>
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="metaeuk" />
+                    <param name="use_augustus_selector" value="metaeuk"/>
                 </conditional>
             </conditional>
-            <param name="outputs" value="short_summary,missing,image,gff" />
+            <param name="outputs" value="short_summary,missing,image,gff"/>
             <output name="busco_sum">
                 <assert_contents>
                     <has_text text="# Gene predictor used: metaeuk"/>
@@ -353,21 +350,21 @@
                 </assert_contents>
             </output>
             <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size"/>
-            <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6" />
+            <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6"/>
         </test>
         <test expect_num_outputs="5">
-            <param name="input" value="genome.fa" />
+            <param name="input" value="genome.fa"/>
             <conditional name="lineage">
-                <param name="lineage_mode" value="auto_detect" />
-                <param name="auto_lineage" value="--auto-lineage" />
+                <param name="lineage_mode" value="auto_detect"/>
+                <param name="auto_lineage" value="--auto-lineage"/>
             </conditional>
             <conditional name="busco_mode">
-                <param name="mode" value="geno" />
+                <param name="mode" value="geno"/>
                 <conditional name="use_augustus">
-                    <param name="use_augustus_selector" value="metaeuk" />
+                    <param name="use_augustus_selector" value="metaeuk"/>
                 </conditional>
             </conditional>
-            <param name="outputs" value="short_summary,missing,image,gff" />
+            <param name="outputs" value="short_summary,missing,image,gff"/>
             <output name="busco_sum">
                 <assert_contents>
                     <has_text text="Gene predictor used: metaeuk"/>
@@ -385,22 +382,22 @@
                     <has_text text="The lineage dataset is: eukaryota_odb10"/>
                 </assert_contents>
             </output>
-            <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
-            <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />
+            <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size"/>
+            <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff"/>
         </test>
         <test expect_num_outputs="3">
-            <param name="input" value="genome.fa" />
+            <param name="input" value="genome.fa"/>
             <conditional name="lineage">
-                <param name="lineage_mode" value="select_lineage" />
-                <param name="lineage_dataset" value="arthropoda_odb10" />
+                <param name="lineage_mode" value="select_lineage"/>
+                <param name="lineage_dataset" value="arthropoda_odb10"/>
             </conditional>
-            <param name="outputs" value="short_summary,gff" />
+            <param name="outputs" value="short_summary,gff"/>
             <output name="busco_sum">
                 <assert_contents>
                     <has_text text="# Gene predictor used: miniprot"/>
                 </assert_contents>
             </output>
-            <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff" />
+            <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff"/>
             <output name="busco_table" file="genome_results_miniprot/full_table">
                 <assert_contents>
                     <has_text text="# BUSCO version is: @TOOL_VERSION@"/>
@@ -412,7 +409,7 @@
     <help><![CDATA[
 
 
-BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
+BUSCO: Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
 --------------------------------------------------------------------------------------------------------------
 
 Interpreting the results
@@ -432,11 +429,11 @@
 is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples
 is what you will be aiming for.
 
-For more information please refer to the Busco_ `user guide <https: / /busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_
+For more information please refer to the Busco_ `user guide <https://busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_
 .
 
 .. _BUSCO: http://busco.ezlab.org/
 
-    ]]>    </help>
-    <expand macro="citations" />
+    ]]></help>
+    <expand macro="citations"/>
 </tool>