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comparison ncbi_fcs_gx.xml @ 4:32d058f3462a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx commit 9da8f86f11185d6bd75ce10de108278db2256bfd
author iuc
date Thu, 21 Nov 2024 02:20:02 +0000
parents ed1ef564da41
children
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3:ed1ef564da41 4:32d058f3462a
10 #set manifest_pathname = $mode.config_tag.fields.local_manifest 10 #set manifest_pathname = $mode.config_tag.fields.local_manifest
11 #if $mode.config_tag.fields.use_source_manifest == "1" 11 #if $mode.config_tag.fields.use_source_manifest == "1"
12 #set manifest_pathname = $mode.config_tag.fields.source_manifest 12 #set manifest_pathname = $mode.config_tag.fields.source_manifest
13 #end if 13 #end if
14 ## skip checksumming the database if the db_state_file exists 14 ## skip checksumming the database if the db_state_file exists
15 if [ ! -e '\${TMPDIR}/sync-files-completed.txt' ]; then 15 if [ ! -e "\${TMPDIR}/sync-files-completed.txt" ]; then
16 ## copy data to local storage 16 ## copy data to local storage
17 mkdir -p '\${TMPDIR}' && 17 mkdir -p "\${TMPDIR}" &&
18 sync_files.py get --mft '$manifest_pathname' --dir '\${TMPDIR}' > /dev/null 2>&1 && 18 sync_files.py get --mft '$manifest_pathname' --dir "\${TMPDIR}" > /dev/null 2>&1 &&
19 touch '\${TMPDIR}/sync-files-completed.txt'; 19 touch "\${TMPDIR}/sync-files-completed.txt";
20 fi && 20 fi &&
21 ## run gx 21 ## run gx
22 GX_NUM_CORES=\${GALAXY_SLOTS:-2} run_gx.py 22 GX_NUM_CORES=\${GALAXY_SLOTS:-2} run_gx.py
23 #if $mode.config_tag.fields.phone_home == "1" 23 #if $mode.config_tag.fields.phone_home == "1"
24 --phone-home-label '$mode.config_tag.fields.phone_home_label' 24 --phone-home-label '$mode.config_tag.fields.phone_home_label'
35 #end if 35 #end if
36 --split-fasta '$mode.screen_adv.split_fasta' 36 --split-fasta '$mode.screen_adv.split_fasta'
37 #if $mode.screen_adv.div: 37 #if $mode.screen_adv.div:
38 --div '$mode.screen_adv.div' 38 --div '$mode.screen_adv.div'
39 #end if 39 #end if
40 --gx-db '\${TMPDIR}' 40 --gx-db "\${TMPDIR}"
41 --out-basename output 41 --out-basename output
42 --action-report true 42 --action-report true
43 --generate-logfile false 43 --generate-logfile false
44 #elif $mode.mode_selector == "clean" 44 #elif $mode.mode_selector == "clean"
45 ## run gx 45 ## run gx