Mercurial > repos > iuc > hal_halstats
comparison hal_halStats.xml @ 1:a9eb29f924e1 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit f46096b336bf460424143fc9d633b5e7c20bf1cf
| author | iuc |
|---|---|
| date | Thu, 05 Mar 2026 11:30:42 +0000 |
| parents | a9c52b2edba7 |
| children |
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| 0:a9c52b2edba7 | 1:a9eb29f924e1 |
|---|---|
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 <expand macro="stdio"/> | 7 <expand macro="stdio"/> |
| 8 <command detect_errors="aggressive"><![CDATA[ | 8 <command detect_errors="aggressive"><![CDATA[ |
| 9 set -o pipefail; ## Sets the pipeline’s exit code to halStats’s on failure. | 9 set -o pipefail; ## Sets the pipeline’s exit code to halStats’s on failure. |
| 10 ( ## echo headers for specific numerical data | 10 ## echo headers for specific numerical data |
| 11 #if $mode.option == '--baseComp': | 11 #if $mode.option == '--baseComp': |
| 12 echo -e 'fraction_of_As\tfraction_of_Gs\tfraction_of_Cs\tfraction_of_Ts'; | 12 echo -e 'fraction_of_As\tfraction_of_Gs\tfraction_of_Cs\tfraction_of_Ts' >> '$out_file' && |
| 13 #else if $mode.option == '--numSegments': | 13 #else if $mode.option == '--numSegments': |
| 14 echo -e 'numTopSegments\tnumBottomSegments'; | 14 echo -e 'numTopSegments\tnumBottomSegments' >> '$out_file' && |
| 15 #end if | 15 #end if |
| 16 halStats | 16 halStats |
| 17 #if $mode.option == '--allCoverage': | 17 #if $mode.option == '--allCoverage': |
| 18 --allCoverage | 18 --allCoverage |
| 19 #else if $mode.option == '--branches': | 19 #else if $mode.option == '--branches': |
| 58 --spanRoot '$mode.spanRoot' | 58 --spanRoot '$mode.spanRoot' |
| 59 #else if $mode.option == '--topSegments': | 59 #else if $mode.option == '--topSegments': |
| 60 --topSegments '$mode.topSegments' | 60 --topSegments '$mode.topSegments' |
| 61 #end if | 61 #end if |
| 62 '$input_hal' | 62 '$input_hal' |
| 63 ## Pipes specific output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree. | 63 ## Pipes specific output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree. |
| 64 #if $mode.option == '--allCoverage' or $mode.option == '--sequenceStats' or $mode.option == '--percentID' or $mode.option == '--coverage': | 64 #if $mode.option == '--allCoverage' or $mode.option == '--sequenceStats' or $mode.option == '--percentID' or $mode.option == '--coverage': |
| 65 | tr ',' '\t' | 65 | tr ',' '\t' |
| 66 #else if $mode.option == '--numSegments': | 66 #else if $mode.option == '--numSegments': |
| 67 | tr ' ' '\t' ## Replace spaces | 67 | tr ' ' '\t' ## Replace spaces |
| 68 #end if | 68 #end if |
| 69 ) > '$out_file' | 69 >> '$out_file' |
| 70 ]]></command> | 70 ]]></command> |
| 71 <inputs> | 71 <inputs> |
| 72 <expand macro="input_hal"/> | 72 <expand macro="input_hal"/> |
| 73 <conditional name="mode"> | 73 <conditional name="mode"> |
| 74 <param name="option" type="select" label="Select the type of statistics you are interested in"> | 74 <param name="option" type="select" label="Select the type of statistics you are interested in"> |