# HG changeset patch
# User pimarin
# Date 1690120454 0
# Node ID 73aea20004ff2f48f9b58bfd548349d1ab88a6ba
# Parent  99499a61fa9e3808096819bbe31d077753b9f674
planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty

diff -r 99499a61fa9e -r 73aea20004ff abromics_galaxy_json_extractor.xml
--- a/abromics_galaxy_json_extractor.xml	Sun Jul 23 13:38:12 2023 +0000
+++ b/abromics_galaxy_json_extractor.xml	Sun Jul 23 13:54:14 2023 +0000
@@ -70,12 +70,12 @@
             #if str($tool.select_tool.plot_file_path) != 'None'
                 --plot_file_path '$tool.select_tool.plot_file_path'
                 --plot_file_hid '$tool.select_tool.plot_file_path.hid'
-            #end if 
+            #end if
         #elif $tool.select_tool.tool_list == "bandage"
             #if str($tool.select_tool.bandage_plot_path) != 'None'
                 --bandage_plot_path '$tool.select_tool.bandage_plot_path'
                 --bandage_plot_hid '$tool.select_tool.bandage_plot_path.hid'
-            #end if        
+            #end if
         #elif $tool.select_tool.tool_list == "bracken"
             #if str($tool.select_tool.kraken_report_path) != 'None'
                 --kraken_report_path "$tool.select_tool.kraken_report_path"
@@ -126,7 +126,7 @@
         #elif $tool.select_tool.tool_list == "kraken2"
             #if str($tool.select_tool.seq_classification_file_path) != 'None'
                 --seq_classification_file_path "$tool.select_tool.seq_classification_file_path"
-                --seq_classification_file_hid "$tool.select_tool.seq_classification_file_path.hid"      
+                --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.genome_hit_path) != 'None'
@@ -186,7 +186,7 @@
             &&
         #end if
     #end for
-        && ls abromics_extracted_folder 
+        && ls abromics_extracted_folder
         ]]>
     </command>
     <inputs>
@@ -242,10 +242,10 @@
                         <param name="input" type="data" format="txt,tabular" multiple="false" label="Bracken report file" help="Tabular file from bracken output"/>
                         <expand macro="analysis_software_version"/>
                         <expand macro="reference_database_version"/>
-                        <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" label="Kraken re-estimated report" help="New kraken report from bracken tool"/>
+                        <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Kraken re-estimated report" help="New kraken report from bracken tool"/>
                         <param argument="--threshold" type="integer" min="0" optional="true" label="PRIOR on read numbers" help="Prior of read for estimation, default is 0"/>
                         <param argument="--read_len" type="integer" min="0" optional="true" label="Read length"/>
-                        <param argument="--level" type="select" label="Taxonomic level estimation" help="Level of final abundance (from Domain to subspecies, default on species)">
+                        <param argument="--level" type="select" label="Taxonomic level estimation" optional="true" help="Level of final abundance (from Domain to subspecies, default on species)">
                             <option value="D">Domain</option>
                             <option value="P">Phylum</option>
                             <option value="C">Class</option>
@@ -260,13 +260,13 @@
                         <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/>
                         <param argument="--trimmed_forward_R1_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R1" help="trimmed file R1"/>
                         <param argument="--trimmed_reverse_R2_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R2" help="trimmed file R2"/>
-                        <param argument="--html_report_path" type="data" format="html" multiple="false" label="Fastp report html" help="Fastp result in html format"/>
+                        <param argument="--html_report_path" type="data" format="html" multiple="false" optional="true" label="Fastp report html" help="Fastp result in html format"/>
                         <expand macro="analysis_software_version"/>
                         <expand macro="reference_database_version"/>
                     </when>
                     <when value="integronfinder2">
                         <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/>
-                        <param argument="--summary_file_path" type="data" format="txt,tabular" multiple="false" label="Summary report" help="Summary file from integronfinder2"/>
+                        <param argument="--summary_file_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Summary report" help="Summary file from integronfinder2"/>
                         <expand macro="analysis_software_version"/>
                         <expand macro="reference_database_version"/>
                     </when>
@@ -300,7 +300,7 @@
                     </when>
                     <when value="quast">
                         <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/>
-                        <param argument="--quast_html_path" type="data" format="html" multiple="false" label="Quast html report" help="Quast html report"/>
+                        <param argument="--quast_html_path" type="data" format="html" multiple="false" optional="true" label="Quast html report" help="Quast html report"/>
                         <expand macro="analysis_software_version"/>
                         <expand macro="reference_database_version"/>
                     </when>
@@ -334,7 +334,7 @@
                     </when>
                     <when value="tabular_file">
                         <param name="input" type="data" format="txt,tabular" multiple="false" label="Tabular file type" help="Generic result file in tabular format with header"/>
-                        <param argument="--analysis_software_name" type="text" multiple="false" label="Tool name" help="Tool name which generated the result file"/>
+                        <param argument="--analysis_software_name" type="text" multiple="false" optional="true" label="Tool name" help="Tool name which generated the result file"/>
                         <expand macro="analysis_software_version"/>
                         <expand macro="reference_database_version"/>
                     </when>