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comparison presto_maskprimers.xml @ 4:df0797c61790 draft default tip

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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"/>