Mercurial > repos > iuc > presto_filterseq

comparison presto_filterseq.xml @ 4:4a4e086f6e38 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 09:02:30 +0000
parents 196b83ac37f2
children
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3:196b83ac37f2 4:4a4e086f6e38
1 <tool id="presto_filterseq" name="pRESTO FilterSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="presto_filterseq" name="pRESTO FilterSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Filters and/or masks reads based on length, quality, missing bases and repeats.</description> 2 <description>Filters and/or masks reads based on length, quality, missing bases and repeats.</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>FilterSeq.py --version</version_command> 10 <version_command>FilterSeq.py --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
76 <data name="fastq_out" format="fastq"/> 76 <data name="fastq_out" format="fastq"/>
77 <expand macro="presto-log-output"/> 77 <expand macro="presto-log-output"/>
78 </outputs> 78 </outputs>
79 79
80 <tests> 80 <tests>
81 <test> 81 <test expect_num_outputs="1">
82 <param name="command" value="length"/> 82 <param name="command" value="length"/>
83 <param name="n" value="299"/> 83 <param name="n" value="299"/>
84 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> 84 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
85 <output name="fastq_out" file="presto_filterseq_length_test_out.fastq" sort="true"/> 85 <output name="fastq_out" file="presto_filterseq_length_test_out.fastq" sort="true"/>
86 </test> 86 </test>
87 <test> 87 <test expect_num_outputs="1">
88 <param name="command" value="missing"/> 88 <param name="command" value="missing"/>
89 <param name="n" value="281"/> 89 <param name="n" value="281"/>
90 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> 90 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
91 <output name="fastq_out" file="presto_filterseq_missing_test_out.fastq" sort="true"/> 91 <output name="fastq_out" file="presto_filterseq_missing_test_out.fastq" sort="true"/>
92 </test> 92 </test>
93 <test> 93 <test expect_num_outputs="1">
94 <param name="command" value="repeats"/> 94 <param name="command" value="repeats"/>
95 <param name="n" value="8"/> 95 <param name="n" value="8"/>
96 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> 96 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
97 <output name="fastq_out" file="presto_filterseq_repeats_test_out.fastq" sort="true"/> 97 <output name="fastq_out" file="presto_filterseq_repeats_test_out.fastq" sort="true"/>
98 </test> 98 </test>
99 <test> 99 <test expect_num_outputs="1">
100 <param name="command" value="quality"/> 100 <param name="command" value="quality"/>
101 <param name="q" value="30"/> 101 <param name="q" value="30"/>
102 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> 102 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
103 <output name="fastq_out" file="presto_filterseq_quality_test_out.fastq" sort="true"/> 103 <output name="fastq_out" file="presto_filterseq_quality_test_out.fastq" sort="true"/>
104 </test> 104 </test>
105 <test> 105 <test expect_num_outputs="1">
106 <param name="command" value="maskqual"/> 106 <param name="command" value="maskqual"/>
107 <param name="q" value="30"/> 107 <param name="q" value="30"/>
108 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> 108 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
109 <output name="fastq_out" file="presto_filterseq_maskqual_test_out.fastq" sort="true"/> 109 <output name="fastq_out" file="presto_filterseq_maskqual_test_out.fastq" sort="true"/>
110 </test> 110 </test>
111 <test> 111 <test expect_num_outputs="1">
112 <param name="command" value="trimqual"/> 112 <param name="command" value="trimqual"/>
113 <param name="q" value="30"/> 113 <param name="q" value="30"/>
114 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> 114 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/>
115 <output name="fastq_out" file="presto_filterseq_trimqual_test_out.fastq" sort="true"/> 115 <output name="fastq_out" file="presto_filterseq_trimqual_test_out.fastq" sort="true"/>
116 </test> 116 </test>