diff abromics_galaxy_json_extractor.xml @ 6:089c8dda0782 draft

planemo upload for repository https://gitlab.com/ifb-elixirfr/abromics/galaxy-tools commit e7d9e8f7411e216a9e5277803854d23dba615504
author ifb-elixirfr
date Sun, 15 Oct 2023 08:34:08 +0000
parents e58c2cd8e624
children fe7c0554432c
line wrap: on
line diff
--- a/abromics_galaxy_json_extractor.xml	Fri Oct 06 13:42:25 2023 +0000
+++ b/abromics_galaxy_json_extractor.xml	Sun Oct 15 08:34:08 2023 +0000
@@ -130,6 +130,10 @@
                 --seq_classification_file_hid "$tool.select_tool.seq_classification_file_path.hid"
             #end if
         #elif $tool.select_tool.tool_list == "plasmidfinder"
+            #if str($tool.select_tool.plasmid_result_tabular_path) != 'None'
+                --plasmid_result_tabular_path "$tool.select_tool.plasmid_result_tabular_path"
+                --plasmid_result_tabular_hid "$tool.select_tool.plasmid_result_tabular_path.hid"
+            #end if
             #if str($tool.select_tool.genome_hit_path) != 'None'
                 --genome_hit_path "$tool.select_tool.genome_hit_path"
                 --genome_hit_hid "$tool.select_tool.genome_hit_path.hid"
@@ -164,19 +168,19 @@
         #elif $tool.select_tool.tool_list == "staramr"
             #if str($tool.select_tool.mlst_file_path) != 'None'
                 --mlst_file_path "$tool.select_tool.mlst_file_path"
-                --mlst_hid "$tool.select_tool.mlst_file_path.hid"
+                --mlst_file_hid "$tool.select_tool.mlst_file_path.hid"
             #end if
             #if str($tool.select_tool.plasmidfinder_file_path) != 'None'
                 --plasmidfinder_file_path "$tool.select_tool.plasmidfinder_file_path"
-                --plasmidfinder_hid "$tool.select_tool.plasmidfinder_file_path.hid"
+                --plasmidfinder_file_hid "$tool.select_tool.plasmidfinder_file_path.hid"
             #end if
             #if str($tool.select_tool.pointfinder_file_path) != 'None'
                 --pointfinder_file_path "$tool.select_tool.pointfinder_file_path"
-                --pointfinder_hid "$tool.select_tool.pointfinder_file_path.hid"
+                --pointfinder_file_hid "$tool.select_tool.pointfinder_file_path.hid"
             #end if
             #if str($tool.select_tool.setting_file_path) != 'None'
                 --setting_file_path "$tool.select_tool.setting_file_path"
-                --setting_hid "$tool.select_tool.setting_file_path.hid"
+                --setting_file_hid "$tool.select_tool.setting_file_path.hid"
             #end if
         #elif $tool.select_tool.tool_list == "tabular_file"
                 --analysis_software_name "$tool.select_tool.analysis_software_name"
@@ -293,6 +297,7 @@
                     </when>
                     <when value="plasmidfinder">
                         <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/>
+                        <param argument="--plasmid_result_tabular_path" type="data" format="tabular" optional="true" multiple="false" label="Result in tabular format" help="Plasmid result in tabular format"/>
                         <param argument="--genome_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/>
                         <param argument="--plasmid_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/>
                         <expand macro="analysis_software_version"/>
@@ -593,27 +598,44 @@
         ** Tool input**
         abromics_galaxy_json_extractor can use several input type from at least 14 different tools :
 
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | Tools          | Version        | Default input file| Optional files                                             |
-        | -:             |   :-:          |  :-               | :-                                                         |
+        +================+================+===================+============================================================+
         | Abricate       | 1.0.1          |  output.tsv       |                                                            |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | Bakta          | 1.7.0          |  output.json      | protein.faa, nucleotide.fna, annotation.gff3, summary.txt  |
+        +----------------+----------------+-------------------+------------------------------------------------------------+        
         | Bandage        | 0.8.1          |  info.txt         |                                                            |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | Bracken        | 2.8            |  output.tsv       | taxonomy.tsv                                               |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | Fastp          | 0.23.2         |  output.json      |                                                            |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | Integronfinder2| 2.0.2          |  output.integrons | output.summary                                             |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | ISEScan        | 1.7.2.3        |  output.tsv       | is.fna, orf.faa, orf.fna                                   |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | Kraken2        | 2.1.2          |  taxonomy.tsv     | reads_assignation.txt                                      |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | Plasmidfinder  | 2.1.6          |  output.json      | genome_hits.fasta, plasmid_hits.fasta                      |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | Quast          | 5.2.0          |  output.tsv       |                                                            |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | Recentrifuge   | 1.10.0         |  data.tsv         | report.html, stat.tsv                                      |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | Refseqmasher   | 0.1.2          |  output.tsv       |                                                            |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | Shovill        | 1.1.0          |  contigs.fasta    | alignment.bam, contigs.gfa                                 |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | Staramr        | 0.9.1          |  resfinder.tsv    | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
         | tabular_file   |  0             |  output.tsv       | no optional files                                          |
+        +----------------+----------------+-------------------+------------------------------------------------------------+
 
         ** Options **
         You can add a tool version and a database version for related tools.
         For some tools you can add optional files previously produced by the tool
+
             ]]></help>
     <expand macro="citations"/>
 </tool>