Mercurial > repos > iuc > colibread_lordec
comparison lordec.xml @ 7:c126b04edfd2 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 747394d19e88a569a5154615e366ea0401c820dd
| author | iuc |
|---|---|
| date | Sat, 05 Oct 2024 19:56:00 +0000 |
| parents | a32b531f66a0 |
| children |
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| 6:a32b531f66a0 | 7:c126b04edfd2 |
|---|---|
| 1 <tool id="lordec" name="Lordec" version="0.9+galaxy2" profile="@PROFILE@"> | 1 <tool id="lordec" name="Lordec" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@"> |
| 2 <description>is a set a programs for correcting sequencing errors in PacBio reads</description> | 2 <description>is a set a programs for correcting sequencing errors in PacBio reads</description> |
| 3 <macros> | 3 <macros> |
| 4 <token name="@TOOL_VERSION@">0.9</token> | |
| 4 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 5 </macros> | 6 </macros> |
| 6 <requirements> | 7 <requirements> |
| 7 <requirement type="package" version="0.9">lordec</requirement> | 8 <requirement type="package" version="@TOOL_VERSION@">lordec</requirement> |
| 8 </requirements> | 9 </requirements> |
| 9 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
| 10 #if str( $program_type_choice.program_type ) == "correct": | 11 #if str( $program_type_choice.program_type ) == "correct": |
| 11 lordec-correct | 12 lordec-correct |
| 12 @lordec_inputs@ | 13 @lordec_inputs@ |
| 61 <expand macro="lordec_inputs" /> | 62 <expand macro="lordec_inputs" /> |
| 62 </when> | 63 </when> |
| 63 </conditional> | 64 </conditional> |
| 64 </inputs> | 65 </inputs> |
| 65 <outputs> | 66 <outputs> |
| 66 <data format="fasta" name="corrected_read_file" label="Corrected long reads with ${tool.name} on ${on_string}" > | 67 <data format="fasta" name="corrected_read_file" label="${tool.name} on ${on_string}: Corrected long reads" > |
| 67 <filter>program_type_choice['program_type'] == 'correct'</filter> | 68 <filter>program_type_choice['program_type'] == 'correct'</filter> |
| 68 </data> | 69 </data> |
| 69 <data format="fasta" name="trimmed_reads_file" label="Trimmed reads file with ${tool.name} on ${on_string}" > | 70 <data format="fasta" name="trimmed_reads_file" label="${tool.name} on ${on_string}: Trimmed reads" > |
| 70 <filter>program_type_choice['program_type'] == 'trim'</filter> | 71 <filter>program_type_choice['program_type'] == 'trim'</filter> |
| 71 </data> | 72 </data> |
| 72 <data format="tabular" name="stat_file" label="Stats with ${tool.name} on ${on_string}" > | 73 <data format="tabular" name="stat_file" label="${tool.name} on ${on_string}: Stats" > |
| 73 <filter>program_type_choice['program_type'] == 'stats'</filter> | 74 <filter>program_type_choice['program_type'] == 'stats'</filter> |
| 74 </data> | 75 </data> |
| 75 </outputs> | 76 </outputs> |
| 76 <tests> | 77 <tests> |
| 77 <test> | 78 <test expect_num_outputs="1"> |
| 78 <conditional name="program_type_choice"> | 79 <conditional name="program_type_choice"> |
| 79 <param name="program_type" value="correct" /> | 80 <param name="program_type" value="correct" /> |
| 80 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" ftype="fasta.gz"/> | 81 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" ftype="fasta.gz"/> |
| 81 <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" /> | 82 <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" /> |
| 82 <param name="k" value="31" /> | 83 <param name="k" value="31" /> |
| 83 </conditional> | 84 </conditional> |
| 84 <output name="corrected_read_file" file="lordec/corrected_reads.fa"/> | 85 <output name="corrected_read_file" file="lordec/corrected_reads.fa"/> |
| 85 </test> | 86 </test> |
| 86 <test> | 87 <test expect_num_outputs="1"> |
| 87 <conditional name="program_type_choice"> | 88 <conditional name="program_type_choice"> |
| 88 <param name="program_type" value="trim" /> | 89 <param name="program_type" value="trim" /> |
| 89 <param name="i" value="lordec/corrected_reads.fa" ftype="fasta"/> | 90 <param name="i" value="lordec/corrected_reads.fa" ftype="fasta"/> |
| 90 </conditional> | 91 </conditional> |
| 91 <output name="trimmed_reads_file" file="lordec/trimmed_reads.fa"/> | 92 <output name="trimmed_reads_file" file="lordec/trimmed_reads.fa"/> |
| 92 </test> | 93 </test> |
| 93 <test> | 94 <test expect_num_outputs="1"> |
| 94 <conditional name="program_type_choice"> | 95 <conditional name="program_type_choice"> |
| 95 <param name="program_type" value="stats" /> | 96 <param name="program_type" value="stats" /> |
| 96 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" /> | 97 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" /> |
| 97 <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" /> | 98 <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" /> |
| 98 </conditional> | 99 </conditional> |