| Previous changeset 3:8d6686664021 (2024-09-30) Next changeset 5:66617be450bd (2025-04-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 301f4d78613f8f6e120b5ed8b56bd5e084e99b13 |
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modified:
macro.xml tooldistillator.xml |
| b |
| diff -r 8d6686664021 -r ea93df4b3df2 macro.xml --- a/macro.xml Mon Sep 30 10:15:57 2024 +0000 +++ b/macro.xml Thu Oct 17 08:00:15 2024 +0000 |
| [ |
| @@ -1,13 +1,22 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">0.9.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.05</token> <xml name="version_command"> <version_command><![CDATA[tooldistillator --version]]></version_command> </xml> <xml name="analysis_software_version"> - <param argument="--analysis_software_version" type="text" optional="true" label="Analysis software version"/> + <conditional name="origin"> + <param name="origin" type="select" label="Has the dataset just been imported?"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true"> + <param argument="--analysis_software_version" type="text" optional="true" label="Analysis software version"/> + </when> + <when value="false"/> + </conditional> </xml> <xml name="reference_database_version"> <param argument="--reference_database_version" type="text" optional="true" label="Database software version"/> |
| b |
| diff -r 8d6686664021 -r ea93df4b3df2 tooldistillator.xml --- a/tooldistillator.xml Mon Sep 30 10:15:57 2024 +0000 +++ b/tooldistillator.xml Thu Oct 17 08:00:15 2024 +0000 |
| [ |
| b'@@ -10,204 +10,230 @@\n <expand macro="version_command"/>\n <command detect_errors="aggressive"><![CDATA[\n #import re\n+set -x pipefail;\n+\n mkdir "tooldistillator_folder" &&\n \n #set $counter = len($tool_section.tools)-1\n #for $i, $tool in enumerate( $tool_section.tools )\n+ #if $tool.select_tool.tool_list == \'staramr\':\n+ln -s \'$tool.select_tool.input\' \'resfinder.tsv\' &&\n+ #if $tool.select_tool.mlst_file_path\n+ln -s \'$tool.select_tool.mlst_file_path\' \'mlst.tsv\' &&\n+ #end if\n+ #if $tool.select_tool.plasmidfinder_file_path\n+ln -s \'$tool.select_tool.plasmidfinder_file_path\' \'plasmidfinder.tsv\' &&\n+ #end if\n+ #if $tool.select_tool.pointfinder_file_path\n+ln -s \'$tool.select_tool.pointfinder_file_path\' \'pointfinder.tsv\' &&\n+ #end if\n+ #if $tool.select_tool.setting_file_path\n+ln -s \'$tool.select_tool.setting_file_path\' \'setting.tsv\' &&\n+ #end if\n+ #end if\n+\n tooldistillator\n- $tool.select_tool.tool_list\n- --hid \'$tool.select_tool.input.hid\'\n- \'$tool.select_tool.input\'\n- --analysis_software_version \'$tool.select_tool.analysis_software_version\'\n- --reference_database_version \'$tool.select_tool.reference_database_version\'\n+ $tool.select_tool.tool_list\n+ --hid \'$tool.select_tool.input.hid\'\n+ #if $tool.select_tool.tool_list == \'staramr\':\n+ \'resfinder.tsv\'\n+ #else\n+ \'$tool.select_tool.input\'\n+ #end if\n+ #if $tool.select_tool.origin.origin == \'true\':\n+ --analysis_software_version \'$tool.select_tool.origin.analysis_software_version\'\n+ #else\n+ --analysis_software_version \'$tool.select_tool.input.creating_job.tool_version\'\n+ #end if\n+ --reference_database_version \'$tool.select_tool.reference_database_version\'\n #if $tool.select_tool.tool_list == \'amrfinderplus\':\n #if $tool.select_tool.point_mutation_report_path\n- --point_mutation_report_path \'$tool.select_tool.point_mutation_report_path\'\n- --point_mutation_report_hid \'$tool.select_tool.point_mutation_report_path.hid\'\n+ --point_mutation_report_path \'$tool.select_tool.point_mutation_report_path\'\n+ --point_mutation_report_hid \'$tool.select_tool.point_mutation_report_path.hid\'\n #end if\n #if $tool.select_tool.nucleotide_sequence_path\n- --nucleotide_sequence_path \'$tool.select_tool.nucleotide_sequence_path\'\n- --nucleotide_sequence_hid \'$tool.select_tool.nucleotide_sequence_path.hid\'\n+ --nucleotide_sequence_path \'$tool.select_tool.nucleotide_sequence_path\'\n+ --nucleotide_sequence_hid \'$tool.select_tool.nucleotide_sequence_path.hid\'\n #end if\n #elif $tool.select_tool.tool_list == \'bakta\'\n #if $tool.select_tool.annotation_tabular_path\n- --annotation_tabular_path \'$tool.select_tool.annotation_tabular_path\'\n- --annotation_tabular_hid \'$tool.select_tool.annotation_tabular_path.hid\'\n+ --annotation_tabular_path \'$tool.select_tool.annotation_tabular_path\'\n+ --annotation_tabular_hid \'$tool.select_tool.annotation_tabular_path.hid\'\n #end if\n #if $tool.select_tool.annotation_genbank_path\n- --annotation_genbank_path \'$tool.select_tool.annotation_genbank_path\'\n- --annotation_genbank_hid \'$tool.select_tool.annotation_genbank_path.hid\'\n+ --annotation_genbank_path \'$tool.select_tool.annotation_genbank_path\'\n+ --annotation_genbank_hid \'$tool.select_tool.annotation_genbank_path.hid\'\n #end if\n #if $tool.select_tool.annotation_embl_path\n- --annotation_embl_path \'$tool.select_tool.annotation_embl_path\'\n- --annotation_embl_hid \'$tool.select_tool.annotation_embl_path.hid\'\n+ --annotation_embl_path \'$tool.select_tool.annotation_embl_path\'\n+ --annotation_embl_hid \'$tool.select_tool.annotation_embl_path.hid\'\n #end i'..b' </conditional>\n </repeat>\n@@ -638,7 +714,10 @@\n <param name="tool_list" value="quast"/>\n <param name="input" value="quast/quast_result.tsv" ftype="tabular"/>\n <param name="quast_html_path" value="quast/quast_report.html"/>\n- <param name="analysis_software_version" value="0.5.0"/>\n+ <conditional name="origin">\n+ <param name="origin" value="true"/>\n+ <param name="analysis_software_version" value="0.5.0"/>\n+ </conditional>\n <param name="reference_database_version" value=""/>\n </conditional>\n </repeat>\n@@ -648,7 +727,10 @@\n <param name="input" value="recentrifuge/rcf_data.tsv" ftype="tabular"/>\n <param name="rcf_stat_path" value="recentrifuge/rcf_stat.tsv" ftype="tabular"/>\n <param name="rcf_html_path" value="recentrifuge/rcf_report.html"/>\n- <param name="analysis_software_version" value="1.0"/>\n+ <conditional name="origin">\n+ <param name="origin" value="true"/>\n+ <param name="analysis_software_version" value="1.0"/>\n+ </conditional>\n <param name="reference_database_version" value="1.0"/>\n </conditional>\n </repeat>\n@@ -656,7 +738,10 @@\n <conditional name="select_tool">\n <param name="tool_list" value="refseqmasher"/>\n <param name="input" value="refseqmasher/refsesqmasher.tsv" ftype="tabular"/>\n- <param name="analysis_software_version" value="1.0"/>\n+ <conditional name="origin">\n+ <param name="origin" value="true"/>\n+ <param name="analysis_software_version" value="1.0"/>\n+ </conditional>\n <param name="reference_database_version" value="1.0"/>\n </conditional>\n </repeat>\n@@ -666,7 +751,10 @@\n <param name="input" value="shovill/contigs.fa" ftype="fasta"/>\n <param name="contig_graph_path" value="shovill/contigs.gfa" ftype="txt"/>\n <param name="bam_file_path" value="shovill/alignment.bam" ftype="bam"/>\n- <param name="analysis_software_version" value="1.0"/>\n+ <conditional name="origin">\n+ <param name="origin" value="true"/>\n+ <param name="analysis_software_version" value="1.0"/>\n+ </conditional>\n <param name="reference_database_version" value="1.0"/>\n </conditional>\n </repeat>\n@@ -675,7 +763,10 @@\n <param name="tool_list" value="tabular_file"/>\n <param name="input" value="tabular_file/report.tsv" ftype="tabular"/>\n <param name="analysis_software_name" value="test_galaxy"/>\n- <param name="analysis_software_version" value="1.0"/>\n+ <conditional name="origin">\n+ <param name="origin" value="true"/>\n+ <param name="analysis_software_version" value="1.0"/>\n+ </conditional>\n <param name="reference_database_version" value="1.0"/>\n </conditional>\n </repeat>\n@@ -703,7 +794,6 @@\n <expand macro="element_assert" name="tabular_file_19_output" text="NP_814691"/>\n </output_collection>\n </test>\n-\n </tests>\n <help><![CDATA[\n **What it does**\n' |