Mercurial > repos > iuc > ncbi_fcs_gx

changeset 7:5fe428757fab draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx commit a23e39116e96db7282fa796a10e131bb2d91218b
author iuc
date Wed, 24 Sep 2025 13:29:56 +0000
parents 04036a60676b
children
files macros.xml ncbi_fcs_gx.xml
diffstat 2 files changed, 22 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Jun 04 09:08:30 2025 +0000
+++ b/macros.xml	Wed Sep 24 13:29:56 2025 +0000
@@ -6,7 +6,7 @@
         </requirements>
     </xml>
     <token name="@TOOL_VERSION@">0.5.5</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="biotools">
         <xrefs>
--- a/ncbi_fcs_gx.xml	Wed Jun 04 09:08:30 2025 +0000
+++ b/ncbi_fcs_gx.xml	Wed Sep 24 13:29:56 2025 +0000
@@ -11,13 +11,14 @@
     #if $mode.config_tag.fields.use_source_manifest == "1"
         #set manifest_pathname = $mode.config_tag.fields.source_manifest
     #end if
+    GX_DB_DIR="\${TMPDIR}/$mode.config_tag" &&
     ## skip checksumming the database if the db_state_file exists
-    if [ ! -e "\${TMPDIR}/sync-files-completed.txt" ]; then
+    if [ ! -e "\${GX_DB_DIR}/sync-files-completed.txt" ]; then
         ## copy data to local storage
-        mkdir -p "\${TMPDIR}" &&
-        sync_files.py get --mft '$manifest_pathname' --dir "\${TMPDIR}" > sync_files.log 2>&1 ||
+        mkdir -p "\${GX_DB_DIR}" &&
+        sync_files.py get --mft '$manifest_pathname' --dir "\${GX_DB_DIR}" > sync_files.log 2>&1 ||
         { cat sync_files.log >&2 ; false ; } &&
-        touch "\${TMPDIR}/sync-files-completed.txt";
+        touch "\${GX_DB_DIR}/sync-files-completed.txt";
     fi &&
     ## run gx
     GX_NUM_CORES=\${GALAXY_SLOTS:-2} run_gx.py
@@ -41,7 +42,7 @@
     #if $mode.screen_adv.ignore_same_kingdom
         --ignore-same-kingdom
     #end if
-        --gx-db "\${TMPDIR}"
+        --gx-db "\${GX_DB_DIR}"
         --out-basename output
         --action-report true
         --generate-logfile false
@@ -143,19 +144,25 @@
     </outputs>
     <tests>
         <test expect_num_outputs="2">
-            <param name="mode_selector" value="screen"/>
-            <param name="config_tag" value="test" />
-            <param name="id_selector" value="ncbi_tax"/>
-            <param name="fasta" value="fcsgx_test.fa.gz" ftype="fasta"/>
-            <param name="tax_id" value="6973"/>
+            <conditional name="mode">
+                <param name="mode_selector" value="screen"/>
+                <param name="config_tag" value="test" />
+                <param name="fasta" value="fcsgx_test.fa.gz" ftype="fasta"/>
+                <conditional name="id">
+                    <param name="id_selector" value="ncbi_tax"/>
+                    <param name="tax_id" value="6973"/>
+                </conditional>
+                <section name="screen_adv"/>
+            </conditional>
             <output name="taxonomy_report" file="output.taxonomy.rpt" compare="diff" lines_diff="2" />
             <output name="action_report" file="output.fcs_gx_report.txt" compare="diff" lines_diff="2" />
         </test>
         <test expect_num_outputs="2">
-            <param name="mode_selector" value="clean"/>
-            <param name="id_selector" value="ncbi_tax"/>
-            <param name="input" value="fcsgx_test.fa.gz" ftype="fasta"/>
-            <param name="action_report" value="output.fcs_gx_report.txt" ftype="tabular"/>
+            <conditional name="mode">
+                <param name="mode_selector" value="clean"/>
+                <param name="input" value="fcsgx_test.fa.gz" ftype="fasta"/>
+                <param name="action_report" value="output.fcs_gx_report.txt" ftype="tabular"/>
+            </conditional>
             <output name="contam_fasta" decompress="true" file="output.contam.fa.gz" ftype="fasta" />
             <output name="clean_fasta" decompress="true" file="output.clean.fa.gz" ftype="fasta" />
         </test>