Mercurial > repos > iuc > medaka_consensus_pipeline

comparison medaka_consensus.xml @ 3:35666d44fe7a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
author iuc
date Tue, 01 Sep 2020 03:08:04 -0400
parents 6a87478ed985
children a1b70f038b4a
comparison
equal deleted inserted replaced
2:6a87478ed985 3:35666d44fe7a
1 <tool id="medaka_consensus_pipeline" name="medaka: Consensus pipeline" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 1 <tool id="medaka_consensus_pipeline" name="medaka: Consensus pipeline" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
2 <description>Assembly polishing via neural networks</description> 2 <description>Assembly polishing via neural networks</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
17 -t \${GALAXY_SLOTS:-4} 17 -t \${GALAXY_SLOTS:-4}
18 ## required 18 ## required
19 -i '$i' 19 -i '$i'
20 -d '$d' 20 -d '$d'
21 21
22 |& tee '$out_log' 22 2>&1 | tee '$out_log'
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <param argument="-i" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select basecalls"/> 25 <param argument="-i" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select basecalls"/>
26 <param argument="-d" type="data" format="fasta,fasta.gz" label="Select assembly" help="The input assembly should be preprocessed with racon."/> 26 <param argument="-d" type="data" format="fasta,fasta.gz" label="Select assembly" help="The input assembly should be preprocessed with racon."/>
27 <expand macro="model"/> 27 <expand macro="model"/>
74 <has_text_matching expression=".+GTCAGAATCGCGTTCAGCGCGTTTCAGCGGTGCGTACAATT.+"/> 74 <has_text_matching expression=".+GTCAGAATCGCGTTCAGCGCGTTTCAGCGGTGCGTACAATT.+"/>
75 </assert_contents> 75 </assert_contents>
76 </output> 76 </output>
77 <output name="out_probs"> 77 <output name="out_probs">
78 <assert_contents> 78 <assert_contents>
79 <has_size value="192187" delta="100"/> 79 <!-- <has_size value="192187" delta="100"/> -->
80 <has_size value="165271" delta="100"/>
80 </assert_contents> 81 </assert_contents>
81 </output> 82 </output>
82 <output name="out_calls"> 83 <output name="out_calls">
83 <assert_contents> 84 <assert_contents>
84 <has_size value="533242" delta="100"/> 85 <!-- <has_size value="533242" delta="100"/> -->
86 <has_size value="343197" delta="100"/>
85 </assert_contents> 87 </assert_contents>
86 </output> 88 </output>
87 </test> 89 </test>
88 <!-- #2 --> 90 <!-- #2 -->
89 <test expect_num_outputs="7"> 91 <test expect_num_outputs="7">
94 <param name="out" value="consensus,probs,calls,draft,variants,polished,log"/> 96 <param name="out" value="consensus,probs,calls,draft,variants,polished,log"/>
95 <output name="out_consensus"> 97 <output name="out_consensus">
96 <assert_contents> 98 <assert_contents>
97 <has_n_lines n="65"/> 99 <has_n_lines n="65"/>
98 <has_line line=">4 length=3792 depth=114.52x circular=true"/> 100 <has_line line=">4 length=3792 depth=114.52x circular=true"/>
99 <has_line line="CATCTCTTT"/> 101 <has_line line="ATCTCTTT"/>
100 </assert_contents> 102 </assert_contents>
101 </output> 103 </output>
102 <output name="out_probs"> 104 <output name="out_probs">
103 <assert_contents> 105 <assert_contents>
104 <has_size value="192710" delta="100"/> 106 <has_size value="166251" delta="100"/>
107 <!-- <has_size value="192710" delta="100"/> -->
105 </assert_contents> 108 </assert_contents>
106 </output> 109 </output>
107 <output name="out_calls"> 110 <output name="out_calls">
108 <assert_contents> 111 <assert_contents>
109 <has_size value="533163" delta="100"/> 112 <has_size value="343197" delta="100"/>
113 <!-- <has_size value="533163" delta="100"/> -->
110 </assert_contents> 114 </assert_contents>
111 </output> 115 </output>
112 <output name="out_draft"> 116 <output name="out_draft">
113 <assert_contents> 117 <assert_contents>
114 <has_n_lines n="6"/> 118 <has_line line="chain 3788 4 3792 + 0 3792 4 3788 + 0 3788 1"/>
115 <has_line line="chain 3789 4 3792 + 0 3792 4 3789 + 0 3789 1"/> 119 <has_line line="1409 1 0"/>
116 <has_line line="1204"/> 120 <has_line line="440 1 0"/>
121 <has_line line="736 1 0"/>
122 <has_line line="853 1 0"/>
123 <has_line line="350"/>
117 </assert_contents> 124 </assert_contents>
118 </output> 125 </output>
119 <output name="out_polished"> 126 <output name="out_polished">
120 <assert_contents> 127 <assert_contents>
121 <has_size value="9"/> 128 <has_size value="9"/>