Mercurial > repos > iuc > presto_maskprimers
comparison presto_maskprimers.xml @ 4:df0797c61790 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 1beb51cefbe9e6edc8930c7ae0421f28e7bb93c8
| author | iuc |
|---|---|
| date | Fri, 04 Oct 2024 09:04:50 +0000 |
| parents | 98b0b4c22e69 |
| children |
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| 3:98b0b4c22e69 | 4:df0797c61790 |
|---|---|
| 1 <tool id="presto_maskprimers" name="pRESTO MaskPrimers" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | 1 <tool id="presto_maskprimers" name="pRESTO MaskPrimers" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 2 <description>Removes primers and annotates sequences with primer and barcode identifiers.</description> | 2 <description>Removes primers and annotates sequences with primer and barcode identifiers.</description> |
| 3 <expand macro="bio_tools"/> | |
| 4 <macros> | 3 <macros> |
| 5 <import>presto_macros.xml</import> | 4 <import>presto_macros.xml</import> |
| 6 </macros> | 5 </macros> |
| 6 <expand macro="bio_tools"/> | |
| 7 | 7 |
| 8 <expand macro="requirements"/> | 8 <expand macro="requirements"/> |
| 9 | 9 |
| 10 <version_command>MaskPrimers.py --version</version_command> | 10 <version_command>MaskPrimers.py --version</version_command> |
| 11 <command detect_errors="exit_code"><![CDATA[ | 11 <command detect_errors="exit_code"><![CDATA[ |
| 70 <data name="fastq_out" format="fastq" from_work_dir="tmp_mask_primers-pass.fastq"/> | 70 <data name="fastq_out" format="fastq" from_work_dir="tmp_mask_primers-pass.fastq"/> |
| 71 <expand macro="presto-log-output"/> | 71 <expand macro="presto-log-output"/> |
| 72 </outputs> | 72 </outputs> |
| 73 | 73 |
| 74 <tests> | 74 <tests> |
| 75 <test> | 75 <test expect_num_outputs="1"> |
| 76 <param name="command" value="score"/> | 76 <param name="command" value="score"/> |
| 77 <param name="fastq_in" value="presto_maskprimers_without_barcode_test_in.fastq"/> | 77 <param name="fastq_in" value="presto_maskprimers_without_barcode_test_in.fastq"/> |
| 78 <param name="start" value="0"/> | 78 <param name="start" value="0"/> |
| 79 <param name="primers_in" value="read1_primers.fasta"/> | 79 <param name="primers_in" value="read1_primers.fasta"/> |
| 80 <param name="mode" value="cut"/> | 80 <param name="mode" value="cut"/> |
| 81 <param name="maxerror" value="0.15"/> | 81 <param name="maxerror" value="0.15"/> |
| 82 <output name="fastq_out" file="presto_maskprimers_without_barcode_test_score_out.fastq" sort="true"/> | 82 <output name="fastq_out" file="presto_maskprimers_without_barcode_test_score_out.fastq" sort="true"/> |
| 83 </test> | 83 </test> |
| 84 <test> | 84 <test expect_num_outputs="1"> |
| 85 <param name="command" value="score"/> | 85 <param name="command" value="score"/> |
| 86 <param name="fastq_in" value="presto_maskprimers_with_barcode_test_in.fastq"/> | 86 <param name="fastq_in" value="presto_maskprimers_with_barcode_test_in.fastq"/> |
| 87 <param name="start" value="17"/> | 87 <param name="start" value="17"/> |
| 88 <param name="barcode" value="true"/> | 88 <param name="barcode" value="true"/> |
| 89 <param name="primers_in" value="read2_primers.fasta"/> | 89 <param name="primers_in" value="read2_primers.fasta"/> |
| 90 <param name="mode" value="cut"/> | 90 <param name="mode" value="cut"/> |
| 91 <param name="maxerror" value="0.15"/> | 91 <param name="maxerror" value="0.15"/> |
| 92 <output name="fastq_out" file="presto_maskprimers_with_barcode_test_score_out.fastq" sort="true"/> | 92 <output name="fastq_out" file="presto_maskprimers_with_barcode_test_score_out.fastq" sort="true"/> |
| 93 </test> | 93 </test> |
| 94 <test> | 94 <test expect_num_outputs="1"> |
| 95 <param name="command" value="align"/> | 95 <param name="command" value="align"/> |
| 96 <param name="fastq_in" value="presto_maskprimers_without_barcode_test_in.fastq"/> | 96 <param name="fastq_in" value="presto_maskprimers_without_barcode_test_in.fastq"/> |
| 97 <param name="primers_in" value="read1_primers.fasta"/> | 97 <param name="primers_in" value="read1_primers.fasta"/> |
| 98 <param name="mode" value="cut"/> | 98 <param name="mode" value="cut"/> |
| 99 <param name="maxerror" value="0.15"/> | 99 <param name="maxerror" value="0.15"/> |
| 100 <param name="maxlen" value="25"/> | 100 <param name="maxlen" value="25"/> |
| 101 <output name="fastq_out" file="presto_maskprimers_without_barcode_test_align_out.fastq" sort="true"/> | 101 <output name="fastq_out" file="presto_maskprimers_without_barcode_test_align_out.fastq" sort="true"/> |
| 102 </test> | 102 </test> |
| 103 <test> | 103 <test expect_num_outputs="1"> |
| 104 <param name="command" value="align"/> | 104 <param name="command" value="align"/> |
| 105 <param name="fastq_in" value="presto_maskprimers_with_barcode_test_in.fastq"/> | 105 <param name="fastq_in" value="presto_maskprimers_with_barcode_test_in.fastq"/> |
| 106 <param name="barcode" value="true"/> | 106 <param name="barcode" value="true"/> |
| 107 <param name="primers_in" value="read2_primers.fasta"/> | 107 <param name="primers_in" value="read2_primers.fasta"/> |
| 108 <param name="mode" value="cut"/> | 108 <param name="mode" value="cut"/> |