Mercurial > repos > iuc > stacks_pstacks

comparison stacks_pstacks.xml @ 8:f42f9ae6d109 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
author iuc
date Thu, 27 Apr 2017 04:17:39 -0400
parents c9413b0ba604
children 67cbd80b83f5
comparison
equal deleted inserted replaced
7:880c3cb5a5a6 8:f42f9ae6d109
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <command><![CDATA[ 8 <command><![CDATA[
9 #from os.path import splitext 9
10 #import re 10 @CLEAN_EXT@
11 11
12 mkdir stacks_inputs stacks_outputs 12 mkdir stacks_inputs stacks_outputs
13 13
14 && 14 &&
15 15
16 #if $sample.is_of_type('sam'): 16 #if $sample.is_of_type('sam')
17 #set $data_path = splitext($sample.element_identifier)[0] 17 #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".sam"
18 #set $data_path = re.sub(r'\.1$', '', $data_path)
19 #set $data_path = "stacks_inputs/" + $data_path + ".sam"
20 #set inputype = "sam" 18 #set inputype = "sam"
21 #else: 19 #else
22 #set $data_path = splitext($sample.element_identifier)[0] 20 #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".bam"
23 #set $data_path = re.sub(r'\.1$', '', $data_path)
24 #set $data_path = "stacks_inputs/" + $data_path + ".bam"
25 #set inputype = "bam" 21 #set inputype = "bam"
26 #end if 22 #end if
27 23
28 ln -s "${sample}" "${data_path}" 24 ln -s '${sample}' '${data_path}'
29 25
30 && 26 &&
31 27
32 pstacks 28 pstacks
33 29
40 ## Batch description 36 ## Batch description
41 -i $sample_id 37 -i $sample_id
42 38
43 -m $m 39 -m $m
44 40
41 --max_clipped $max_clipped
42 --min_mapq $min_mapq
43 $keep_sec_alns
44
45 ## snp_model 45 ## snp_model
46 #if str( $snp_options.select_model.model_type) == "bounded": 46 #if str( $snp_options.select_model.model_type) == "bounded"
47 --model_type bounded 47 --model_type bounded
48 --bound_low $snp_options.select_model.bound_low 48 --bound_low $snp_options.select_model.bound_low
49 --bound_high $snp_options.select_model.bound_high 49 --bound_high $snp_options.select_model.bound_high
50 --alpha $snp_options.select_model.alpha 50 --alpha $snp_options.select_model.alpha
51 #else if str( $snp_options.select_model.model_type) == "snp": 51 #else if str( $snp_options.select_model.model_type) == "snp"
52 --model_type snp 52 --model_type snp
53 --alpha $snp_options.select_model.alpha 53 --alpha $snp_options.select_model.alpha
54 #else 54 #else
55 --model_type fixed 55 --model_type fixed
56 --bc_err_freq $bc_err_freq 56 --bc_err_freq $bc_err_freq
57 #end if 57 #end if
58 58
59 -o stacks_outputs 59 -o stacks_outputs
60 60
61 > pstacks.log 2>&1 61 2>&1 | tee pstacks.log
62 62
63 ## If input is in bam format, stacks will output gzipped files (no option to control this) 63 ## If input is in bam format, stacks will output gzipped files (no option to control this)
64 && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi 64 && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi
65
66 &&
67
68 stacks_summary.py --stacks-prog pstacks --res-dir stacks_outputs --logfile pstacks.log --summary stacks_outputs/summary.html
65 ]]></command> 69 ]]></command>
66 70
67 <inputs> 71 <inputs>
68 <param name="sample" argument="-f" format="fastqsanger,fasta" type="data" label="Input short reads from an individual" /> 72 <param name="sample" argument="-f" format="sam,bam" type="data" label="Input short reads from an individual" />
69 73
70 <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/> 74 <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/>
71 75
72 <param name="m" argument="-m" type="integer" value="1" label="Minimum depth of coverage required to create a stack"/> 76 <param name="m" argument="-m" type="integer" value="1" label="Minimum depth of coverage required to create a stack"/>
73 77
78 <param name="max_clipped" argument="--max_clipped" type="float" value="0.15" min="0.0" max="1.0" label="Alignments with more than this fraction of soft-clipped bases are discarded"/>
79
80 <param name="min_mapq" argument="--min_mapq" type="integer" value="10" label="Minimum required mapping quality"/>
81
82 <param name="keep_sec_alns" argument="--keep_sec_alns" type="boolean" checked="false" truevalue="--keep_sec_alns" falsevalue="" label="Keep secondary alignments" />
74 83
75 <!-- SNP Model options --> 84 <!-- SNP Model options -->
76 <section name="snp_options" title="SNP Model Options (pstacks options)" expanded="False"> 85 <section name="snp_options" title="SNP Model Options (pstacks options)" expanded="False">
77 <expand macro="snp_options_full"/> 86 <expand macro="snp_options_full"/>
78 </section> 87 </section>
79 </inputs> 88 </inputs>
80 89
81 <outputs> 90 <outputs>
82 <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" /> 91 <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" />
92
93 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" />
94
83 <collection name="tabs" type="list" label="Stacks from ${on_string}"> 95 <collection name="tabs" type="list" label="Stacks from ${on_string}">
84 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> 96 <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
85 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> 97 <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
86 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> 98 <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
87 <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" /> 99 <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" />
94 <param name="sample_id" value="4" /> 106 <param name="sample_id" value="4" />
95 107
96 <output name="output_log"> 108 <output name="output_log">
97 <assert_contents> 109 <assert_contents>
98 <has_text text="done." /> 110 <has_text text="done." />
111 </assert_contents>
112 </output>
113 <output name="output_summary">
114 <assert_contents>
115 <has_text text="Stacks Statistics" />
99 </assert_contents> 116 </assert_contents>
100 </output> 117 </output>
101 118
102 <output_collection name="tabs"> 119 <output_collection name="tabs">
103 <element name="PopA_01.tags"> 120 <element name="PopA_01.tags">