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comparison presto_assemblepairs.xml @ 4:af855eb44091 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 09:04:05 +0000
parents 540fcbdac82e
children
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3:540fcbdac82e 4:af855eb44091
1 <tool id="presto_assemblepairs" name="pRESTO AssemblePairs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="presto_assemblepairs" name="pRESTO AssemblePairs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Assembles paired-end reads into a single sequence.</description> 2 <description>Assembles paired-end reads into a single sequence.</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>presto_macros.xml</import> 4 <import>presto_macros.xml</import>
6 <xml name="align-params"> 5 <xml name="align-params">
7 <param argument="--alpha" type="float" value="1e-05" label="Alpha" help="Significance threshold for de-novo assembly."/> 6 <param argument="--alpha" type="float" value="1e-05" label="Alpha" help="Significance threshold for de-novo assembly."/>
8 <param argument="--maxerror" type="float" value="0.3" label="Max Error" help="Maximum error rate for de novo assembly."/> 7 <param argument="--maxerror" type="float" value="0.3" label="Max Error" help="Maximum error rate for de novo assembly."/>
21 <option value="blastn">Blast</option> 20 <option value="blastn">Blast</option>
22 <option value="usearch">USearch</option> 21 <option value="usearch">USearch</option>
23 </param> 22 </param>
24 </xml> 23 </xml>
25 </macros> 24 </macros>
25 <expand macro="bio_tools"/>
26 26
27 <expand macro="requirements"/> 27 <expand macro="requirements"/>
28 28
29 <version_command>AssemblePairs.py --version</version_command> 29 <version_command>AssemblePairs.py --version</version_command>
30 <command detect_errors="exit_code"><![CDATA[ 30 <command detect_errors="exit_code"><![CDATA[
121 <data name="fastq_out" format="fastq" from_work_dir="tmp_assemble-pass.fastq"/> 121 <data name="fastq_out" format="fastq" from_work_dir="tmp_assemble-pass.fastq"/>
122 <expand macro="presto-log-output"/> 122 <expand macro="presto-log-output"/>
123 </outputs> 123 </outputs>
124 124
125 <tests> 125 <tests>
126 <test> 126 <test expect_num_outputs="1">
127 <param name="command" value="join"/> 127 <param name="command" value="join"/>
128 <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/> 128 <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/>
129 <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/> 129 <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/>
130 <param name="coord" value="presto"/> 130 <param name="coord" value="presto"/>
131 <param name="rc" value="tail"/> 131 <param name="rc" value="tail"/>
133 <param name="r2_annotations" value="PRCONS CONSCOUNT"/> 133 <param name="r2_annotations" value="PRCONS CONSCOUNT"/>
134 <param name="gap" value="10"/> 134 <param name="gap" value="10"/>
135 <output name="fastq_out" file="presto_assemblepairs_test_join_out.fastq" sort="true"/> 135 <output name="fastq_out" file="presto_assemblepairs_test_join_out.fastq" sort="true"/>
136 </test> 136 </test>
137 137
138 <test> 138 <test expect_num_outputs="1">
139 <param name="command" value="align"/> 139 <param name="command" value="align"/>
140 <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/> 140 <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/>
141 <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/> 141 <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/>
142 <param name="coord" value="presto"/> 142 <param name="coord" value="presto"/>
143 <param name="rc" value="tail"/> 143 <param name="rc" value="tail"/>
145 <param name="r2_annotations" value="PRCONS CONSCOUNT"/> 145 <param name="r2_annotations" value="PRCONS CONSCOUNT"/>
146 <param name="scanrev" value="true"/> 146 <param name="scanrev" value="true"/>
147 <output name="fastq_out" file="presto_assemblepairs_test_align_out.fastq" sort="true"/> 147 <output name="fastq_out" file="presto_assemblepairs_test_align_out.fastq" sort="true"/>
148 </test> 148 </test>
149 149
150 <test> 150 <test expect_num_outputs="1">
151 <param name="command" value="reference"/> 151 <param name="command" value="reference"/>
152 <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/> 152 <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/>
153 <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/> 153 <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/>
154 <param name="coord" value="presto"/> 154 <param name="coord" value="presto"/>
155 <param name="rc" value="tail"/> 155 <param name="rc" value="tail"/>
158 <param name="r" value="reference_repertoire.fasta"/> 158 <param name="r" value="reference_repertoire.fasta"/>
159 <param name="aligner" value="blastn"/> 159 <param name="aligner" value="blastn"/>
160 <output name="fastq_out" file="presto_assemblepairs_test_reference_out.fastq" sort="true"/> 160 <output name="fastq_out" file="presto_assemblepairs_test_reference_out.fastq" sort="true"/>
161 </test> 161 </test>
162 162
163 <test> 163 <test expect_num_outputs="1">
164 <param name="command" value="sequential"/> 164 <param name="command" value="sequential"/>
165 <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/> 165 <param name="r1_in" value="presto_assemblepairs_test_r1_in.fastq"/>
166 <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/> 166 <param name="r2_in" value="presto_assemblepairs_test_r2_in.fastq"/>
167 <param name="coord" value="presto"/> 167 <param name="coord" value="presto"/>
168 <param name="rc" value="tail"/> 168 <param name="rc" value="tail"/>