Mercurial > repos > pimarin > abromics_galaxy_json_extractor
changeset 3:73aea20004ff draft default tip
planemo upload commit 8721cd95e02dd6b3a02e2eb549cd8ff6b1675ff8-dirty
| author | pimarin |
|---|---|
| date | Sun, 23 Jul 2023 13:54:14 +0000 |
| parents | 99499a61fa9e |
| children | |
| files | abromics_galaxy_json_extractor.xml |
| diffstat | 1 files changed, 10 insertions(+), 10 deletions(-) [+] |
line wrap: on
line diff
--- 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>