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comparison segalign.xml @ 9:08e987868f0f draft

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planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 062a761a340e095ea7ef7ed7cd1d3d55b1fdc5c4
author richard-burhans
date Wed, 10 Jul 2024 17:06:45 +0000 (8 months ago)
parents 150de8a3954a
children ec709ce3d91b
comparison
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8:150de8a3954a 9:08e987868f0f
31 OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-2} 31 OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-2}
32 32
33 ## Mode ---------------------------------------------------------------- 33 ## Mode ----------------------------------------------------------------
34 34
35 #if str($mode.mode_selector) == "segalign" 35 #if str($mode.mode_selector) == "segalign"
36 #if str($mode.gapped_extension_options.nogapped) == "false"
37 mkdir -p "\$(pwd)/work" &&
38 faToTwoBit <(gzip -cdfq '$mode.target') "\$(pwd)/work/ref.2bit" &&
39 faToTwoBit <(gzip -cdfq '$mode.query') "\$(pwd)/work/query.2bit" &&
40 #end if
36 #if str($mode.diagonal_partition_options.diagonal_partition) == "true" 41 #if str($mode.diagonal_partition_options.diagonal_partition) == "true"
37 #set $segalign_mode = "segalign_diagonal_partition" 42 #set $segalign_mode = "segalign_diagonal_partition"
38 ## explicitly calling bash to bypass a pulsar bug 43 ## explicitly calling python to bypass a pulsar bug
39 ## https://github.com/galaxyproject/pulsar/issues/341 44 ## https://github.com/galaxyproject/pulsar/issues/341
40 bash '$__tool_directory__/runner.py' 45 python '$__tool_directory__/runner.py'
41 --output-type tarball 46 --output-type tarball
42 --output-filename fake 47 --output-file '$segalign_diagonal_partition_output'
43 --diagonal-partition 48 --diagonal-partition
44 --num-cpu \${GALAXY_SLOTS:-2} 49 --num-cpu \${GALAXY_SLOTS:-2}
45 --tool_directory '$__tool_directory__' 50 --tool_directory '$__tool_directory__'
46 #else 51 #else
47 #set $segalign_mode = "segalign" 52 #set $segalign_mode = "segalign"
48 bash '$__tool_directory__/runner.py' 53 python '$__tool_directory__/runner.py'
49 --output-type output 54 --output-type output
50 --output-filename foo.maf 55 --output-file '$segalign_output'
51 --num-cpu \${GALAXY_SLOTS:-2} 56 --num-cpu \${GALAXY_SLOTS:-2}
52 --tool_directory '$__tool_directory__' 57 --tool_directory '$__tool_directory__'
53 #end if 58 #end if
54 '$mode.target' 59 '$mode.target'
55 '$mode.query' 60 '$mode.query'
56 #else if str($mode.mode_selector) == "segalign_repeat_masker" 61 #else if str($mode.mode_selector) == "segalign_repeat_masker"
57 #set $segalign_mode = "segalign_repeat_masker" 62 #set $segalign_mode = "segalign_repeat_masker"
58 run_segalign_repeat_masker 63 run_segalign_repeat_masker
59 '$mode.seq_file' 64 '$mode.seq_file'
65 --num_cpu \${GALAXY_SLOTS:-2}
60 #end if 66 #end if
61 67
62 ## Sequence Options ---------------------------------------------------- 68 ## Sequence Options ----------------------------------------------------
63 69
64 --strand '$mode.sequence_options.strand_selector' 70 --strand '$mode.sequence_options.strand_selector'
142 ## .end if 148 ## .end if
143 ## .if $output_format.rplot: 149 ## .if $output_format.rplot:
144 ## && 150 ## &&
145 ## Rscript $r_plot > /dev/null 2>&1 151 ## Rscript $r_plot > /dev/null 2>&1
146 ## .end if 152 ## .end if
147 #if $segalign_mode == "segalign"
148 --output '$segalign_output'
149 #end if
150 #else if $segalign_mode == "segalign_repeat_masker" 153 #else if $segalign_mode == "segalign_repeat_masker"
151 --M '$mode.output_options.M' 154 --M '$mode.output_options.M'
152 --output '$segalign_repeat_masker_output' 155 --output '$segalign_repeat_masker_output'
153 #end if 156 #end if
154 #if str($mode.output_options.markend) == "true" 157 #if str($mode.output_options.markend) == "true"