Mercurial > repos > iuc > stacks2_tsv2bam

comparison stacks_tsv2bam.xml @ 4:69842dd5aa48 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
author iuc
date Wed, 01 Sep 2021 11:32:48 +0000
parents bf0e43ab0416
children a4b4bd84f69e
comparison
equal deleted inserted replaced
3:a9c34a289493 4:69842dd5aa48
1 <tool id="stacks2_tsv2bam" name="Stacks2: tsv2bam" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> 1 <tool id="stacks2_tsv2bam" name="Stacks2: tsv2bam" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
2 <description>Sort reads by RAD locus</description> 2 <description>Sort reads by RAD locus</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">
7 <requirement type="package" version="1.13">samtools</requirement>
8 </expand>
7 <expand macro="version_cmd"/> 9 <expand macro="version_cmd"/>
8 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
9 @FASTQ_INPUT_FUNCTIONS@ 11 @FASTQ_INPUT_FUNCTIONS@
10 12
11 mkdir stacks_inputs stacks_outputs && 13 mkdir stacks_inputs stacks_outputs &&
46 ## - make stdout stderr 48 ## - make stdout stderr
47 ## - move the additional log file 49 ## - move the additional log file
48 2>&1 50 2>&1
49 51
50 && mv stacks_inputs/*matches.bam stacks_outputs 52 && mv stacks_inputs/*matches.bam stacks_outputs
53
54 ## see comment in gstacks
55 && for b in stacks_outputs/*matches.bam; do (samtools view -b "\$b" || true) 2> /dev/null > tmp && mv tmp "\$b"; done
51 ]]></command> 56 ]]></command>
52 57
53 <inputs> 58 <inputs>
54 <expand macro="input_stacks_macro"/> 59 <expand macro="input_stacks_macro"/>
55 <expand macro="input_cat_macro"/> 60 <expand macro="input_cat_macro"/>
64 <expand macro="out_log"/> 69 <expand macro="out_log"/>
65 <expand macro="tsv2bam_outputs_macro"/> 70 <expand macro="tsv2bam_outputs_macro"/>
66 </outputs> 71 </outputs>
67 72
68 <tests> 73 <tests>
69 <!-- test wo paired end data --> 74 <!-- test wo paired end data (this is not the default used in denovomap .. which is used for generating the test data therefore we only test if a list of two bams is generated) -->
70 <test expect_num_outputs="2"> 75 <test expect_num_outputs="2">
71 <param name="input_cat"> 76 <param name="input_cat">
72 <collection type="list"> 77 <collection type="list">
73 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/> 78 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
74 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/> 79 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
91 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/> 96 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/>
92 </collection> 97 </collection>
93 </param> 98 </param>
94 <param name="add_log" value="yes"/> 99 <param name="add_log" value="yes"/>
95 <output name="output_log" ftype="txt" file="tsv2bam/tsv2bam.log" lines_diff="14"/> 100 <output name="output_log" ftype="txt" file="tsv2bam/tsv2bam.log" lines_diff="14"/>
96 <output_collection name="bams" type="list" count="2"> 101 <output_collection name="bams" type="list" count="2"/>
97 <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/> 102 </test>
98 <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/> 103 <!-- test w popmap, w reverse reads as multiple selection -->
99 </output_collection> 104 <test expect_num_outputs="2">
105 <param name="input_cat">
106 <collection type="list">
107 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
108 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
109 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/>
110 </collection>
111 </param>
112 <param name="input_stacks">
113 <collection type="list">
114 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/>
115 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/>
116 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/>
117 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/>
118 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/>
119 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
120 </collection>
121 </param>
122 <param name="input_matches">
123 <collection type="list">
124 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/>
125 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/>
126 </collection>
127 </param>
128 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
129 <param name="input_type|input_type_select" value="single"/>
130 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
131 <param name="add_log" value="yes"/>
132 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
133 <output_collection name="bams" type="list" count="2"/>
100 </test> 134 </test>
101 <!-- test w popmap, w reverse reads as multiple selection --> 135 <!-- test w popmap, w reverse reads as multiple selection -->
102 <test expect_num_outputs="2"> 136 <test expect_num_outputs="2">
103 <param name="input_cat"> 137 <param name="input_cat">
104 <collection type="list"> 138 <collection type="list">