Mercurial > repos > richard-burhans > segalign
comparison segalign.xml @ 16:4966e095e3c3 draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 6cf972d7f1c9ecb097994494a27d00906c6c3e4d
| author | richard-burhans |
|---|---|
| date | Tue, 30 Jul 2024 17:19:56 +0000 |
| parents | 99ee8d6f6815 |
| children | cefa7625d6cb |
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| 15:99ee8d6f6815 | 16:4966e095e3c3 |
|---|---|
| 17 <include path="lastz-cmd.ini"/> | 17 <include path="lastz-cmd.ini"/> |
| 18 <include path="package_output.py"/> | 18 <include path="package_output.py"/> |
| 19 <include path="runner.py"/> | 19 <include path="runner.py"/> |
| 20 </required_files> | 20 </required_files> |
| 21 <command detect_errors="exit_code"><![CDATA[ | 21 <command detect_errors="exit_code"><![CDATA[ |
| 22 ## Convert input to 2bit for lastz ------------------------------------- | 22 ## Convert input sequences to 2bit ------------------------------------- |
| 23 | 23 |
| 24 mkdir -p "\$(pwd)/work" && | 24 mkdir -p "\$(pwd)/work" && |
| 25 faToTwoBit <(gzip -cdfq '$target') "\$(pwd)/work/ref.2bit" && | 25 faToTwoBit <(gzip -cdfq '$target') "\$(pwd)/work/ref.2bit" && |
| 26 faToTwoBit <(gzip -cdfq '$query') "\$(pwd)/work/query.2bit" && | 26 faToTwoBit <(gzip -cdfq '$query') "\$(pwd)/work/query.2bit" && |
| 27 | |
| 28 ## Run SegAlign -------------------------------------------------------- | |
| 27 | 29 |
| 28 ## explicitly calling python to bypass a pulsar bug | 30 ## explicitly calling python to bypass a pulsar bug |
| 29 ## https://github.com/galaxyproject/pulsar/issues/341 | 31 ## https://github.com/galaxyproject/pulsar/issues/341 |
| 30 python '$__tool_directory__/runner.py' | 32 python '$__tool_directory__/runner.py' |
| 31 --output-type tarball | 33 --output-type tarball |
| 75 --noentropy | 77 --noentropy |
| 76 #end if | 78 #end if |
| 77 | 79 |
| 78 ## Gapped Extension Options -------------------------------------------- | 80 ## Gapped Extension Options -------------------------------------------- |
| 79 | 81 |
| 80 --nogapped | |
| 81 --ydrop '$gapped_extension_options.ydrop' | 82 --ydrop '$gapped_extension_options.ydrop' |
| 82 #if str($gapped_extension_options.gappedthresh) != "" | 83 #if str($gapped_extension_options.gappedthresh) != "" |
| 83 --gappedthresh '$gapped_extension_options.gappedthresh' | 84 --gappedthresh '$gapped_extension_options.gappedthresh' |
| 84 #end if | 85 #end if |
| 85 #if str($gapped_extension_options.notrivial) == "true" | 86 #if str($gapped_extension_options.notrivial) == "true" |
| 90 | 91 |
| 91 #if str($output_options.format.format_selector) == "bam" | 92 #if str($output_options.format.format_selector) == "bam" |
| 92 --format '$output_options.format.bam_options' | 93 --format '$output_options.format.bam_options' |
| 93 #else if str($output_options.format.format_selector) == "general_def" | 94 #else if str($output_options.format.format_selector) == "general_def" |
| 94 --format general- | 95 --format general- |
| 96 #else if str($output_options.format.format_selector) == "general_full" | |
| 97 --format 'general-:${output_options.format.fields}' | |
| 98 | |
| 95 #else if str($output_options.format.format_selector) == "maf" | 99 #else if str($output_options.format.format_selector) == "maf" |
| 96 --format '$output_options.format.maf_type' | 100 --format '$output_options.format.maf_type' |
| 97 #else if str($output_options.format.format_selector) == "blastn" | 101 #else if str($output_options.format.format_selector) == "blastn" |
| 98 --format=BLASTN- | 102 --format=BLASTN- |
| 99 #else if str($output_options.format.format_selector) == "general_full" | |
| 100 --format 'general-:${output_options.format.fields}' | |
| 101 #else if str($output_options.format.format_selector) == "differences" | 103 #else if str($output_options.format.format_selector) == "differences" |
| 102 --format=differences | 104 --format=differences |
| 103 #end if | 105 #end if |
| 104 ## todo :: rplot, bam | 106 ## todo :: rplot, bam |
| 105 ## --action:target=multiple | 107 ## --action:target=multiple |
| 106 ## $output_format.rplot | 108 ## $output_format.rplot |
| 107 ## #if str( $output_format.out.format ) == "bam": | 109 ## .if str( $output_format.out.format ) == "bam": |
| 108 ## | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '${output}' | 110 ## | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '${output}' |
| 109 ## #else: | 111 ## .else: |
| 110 ## > '${output}' | 112 ## > '${output}' |
| 111 ## #end if | 113 ## .end if |
| 112 ## #if $output_format.rplot: | 114 ## .if $output_format.rplot: |
| 113 ## && | 115 ## && |
| 114 ## Rscript $r_plot > /dev/null 2>&1 | 116 ## Rscript $r_plot > /dev/null 2>&1 |
| 115 ## #end if | 117 ## .end if |
| 116 | 118 |
| 117 ## System Options ----------------------------------------------------- | 119 ## System Options ----------------------------------------------------- |
| 118 | 120 |
| 119 --wga_chunk_size '$system_options.wga_chunk_size' | 121 --wga_chunk_size '$system_options.wga_chunk_size' |
| 120 --lastz_interval_size '$system_options.lastz_interval_size' | 122 --lastz_interval_size '$system_options.lastz_interval_size' |
| 127 ## Package Output ---------------------------------------------------- | 129 ## Package Output ---------------------------------------------------- |
| 128 | 130 |
| 129 && | 131 && |
| 130 python '$__tool_directory__/package_output.py' | 132 python '$__tool_directory__/package_output.py' |
| 131 --tool_directory '$__tool_directory__' | 133 --tool_directory '$__tool_directory__' |
| 134 --format_selector '$output_options.format.format_selector' | |
| 132 | 135 |
| 133 ]]></command> | 136 ]]></command> |
| 134 <inputs> | 137 <inputs> |
| 135 <param name="target" type="data" format="fasta,fasta.gz" label="Target sequence file in FASTA format"/> | 138 <param name="target" type="data" format="fasta,fasta.gz" label="Target sequence file in FASTA format"/> |
| 136 <param name="query" type="data" format="fasta,fasta.gz" label="Query sequence file in FASTA format"/> | 139 <param name="query" type="data" format="fasta,fasta.gz" label="Query sequence file in FASTA format"/> |