Mercurial > repos > matthias > stacks2_kmerfilter

comparison stacks_kmerfilter.xml @ 3:7aec316566cb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
author matthias
date Tue, 18 Dec 2018 12:50:41 -0500
parents 324a729c257f
children 2277b0b50371
comparison
equal deleted inserted replaced
2:324a729c257f 3:7aec316566cb
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_cmd"/> 8 <expand macro="version_cmd"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10
11 #if $data_type.dt_select == "single" 10 #if $data_type.dt_select == "single"
12
13 #if $data_type.fname.is_of_type('fastqsanger') 11 #if $data_type.fname.is_of_type('fastqsanger')
14 #set $ext = ".fq" 12 #set $ext = ".fq"
15 #set inputype = "fastq" 13 #set inputype = "fastq"
16 #else 14 #else
17 #set $ext = ".fq.gz" 15 #set $ext = ".fq.gz"
18 #set inputype = "gzfastq" 16 #set inputype = "gzfastq"
19 #end if 17 #end if
20
21 ln -s '$data_type.fname' R1$ext && 18 ln -s '$data_type.fname' R1$ext &&
22 #else 19 #elif $data_type.dt_select == "pair"
23
24 #if $data_type.fwd.is_of_type('fastqsanger') 20 #if $data_type.fwd.is_of_type('fastqsanger')
25 #set $ext = ".fq" 21 #set $ext = ".fq"
26 #set inputype = "fastq" 22 #set inputype = "fastq"
27 #else 23 #else
28 #set $ext = ".fq.gz" 24 #set $ext = ".fq.gz"
29 #set inputype = "gzfastq" 25 #set inputype = "gzfastq"
30 #end if 26 #end if
31
32 ln -s '$data_type.fwd' R1$ext && 27 ln -s '$data_type.fwd' R1$ext &&
33 ln -s '$data_type.rev' R2$ext && 28 ln -s '$data_type.rev' R2$ext &&
34 #end if 29 #end if
35 30
36 mkdir clone_outputs 31 mkdir clone_outputs
37 32
38 && 33 &&
39 34
40 clone_filter 35 kmer_filter
41 #if $data_type.dt_select == 'single': 36 #if $data_type.dt_select == 'single':
42 -f R1$ext 37 -f R1$ext
43
44 #else 38 #else
45 -1 R1$ext 39 -1 R1$ext
46 -2 R2$ext 40 -2 R2$ext
47 #end if 41 #end if
48 42 ## TODO $options_kmer_char.read_k_freq
49 -i $inputype 43 -i $inputype
50
51 -o clone_outputs 44 -o clone_outputs
52 $capture 45 $capture
46 -y gzfastq
47 $options_filtering.rare
48 $options_filtering.abundant
49 --k_len $options_filtering.k_len
50 --max_k_freq $options_advanced_filtering.max_k_freq
51 #if str($options_advanced_filtering.min_lim)!="":
52 --min_lim $options_advanced_filtering.min_lim
53 #end if
54 #if str($options_advanced_filtering.max_lim)!="":
55 --max_lim $options_advanced_filtering.max_lim
56 #end if
57 #if str($options_normalization.normalize)!="":
58 --normalize $options_normalization.normalize
59 #end if
60 #if $options_kmer_char.write_k_freq
61 --read_k_freq $kfreq
62 #end if
63 $options_kmer_char.k_dist
64 #if $options_kmer_char.k_dist
65 | sed 's/KmerFrequency/# KmerFrequency/' $kfreqdist>
66 #end if
53 67
54 #if $oligo_len_1
55 --oligo_len_1 $oligo_len_1
56 #end if
57 #if $oligo_len_2
58 --oligo_len_2 $oligo_len_2
59 #end if
60 $data_type.barcode_encoding
61 $retain_oligo
62 -y gzfastq
63 68
64 ]]></command> 69 ]]></command>
65 <inputs> 70 <inputs>
66 <conditional name="data_type"> 71 <conditional name="data_type">
67 <param name="dt_select" type="select" label="Single or Paired-end"> 72 <param name="dt_select" type="select" label="Single or Paired-end">
68 <option value="single">Single</option> 73 <option value="single">Single</option>
69 <option value="pair">Pair</option> 74 <option value="pair">Pair</option>
70 </param> 75 </param>
71 <when value="single"> 76 <when value="single">
72 <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" /> 77 <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" />
73 <param name="barcode_encoding" type="select" label="Barcode location">
74 <expand macro="barcode_encoding_single" />
75 </param>
76
77 </when> 78 </when>
78 <when value="pair"> 79 <when value="pair">
79 <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" /> 80 <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" />
80 <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" /> 81 <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" />
81 <param name="barcode_encoding" type="select" label="Barcode location">
82 <expand macro="barcode_encoding_pair" />
83 </param>
84 </when> 82 </when>
85 </conditional> 83 </conditional>
86 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> 84 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
87 <section name="options_filtering" title="Filtering options" expanded="False"> 85 <section name="options_filtering" title="Filtering options" expanded="False">
88 <param argument="--rare" type="boolean" checked="false" truevalue="--rare" falsevalue="" label="turn on filtering based on rare k-mers" /> 86 <param argument="--rare" type="boolean" checked="false" truevalue="--rare" falsevalue="" label="turn on filtering based on rare k-mers" />
89 <param argument="--abundant" type="boolean" checked="false" truevalue="--abundant" falsevalue="" label="turn on filtering based on abundant k-mers" /> 87 <param argument="--abundant" type="boolean" checked="false" truevalue="--abundant" falsevalue="" label="turn on filtering based on abundant k-mers" />
90 <param argument="--k_len" type="integer" value="15" label="k-mer size" /> 88 <param argument="--k_len" type="integer" value="15" label="k-mer size" />
91 </section> 89 </section>
92 <section name="options_advanced_filtering" title="Advanced fitering options" expanded="False"> 90 <section name="options_advanced_filtering" title="Advanced fitering options" expanded="False">
91 <param argument="--max_k_freq" type="integer" value="20000" label="number of times a kmer must occur to be considered abundant" />
92 <param argument="--min_lim" type="integer" value="" optional="true" label="number of rare kmers occuring in a row required to discard a read" help="(default: 80% of the k-mer length)." />
93 <param argument="--max_lim" type="integer" value="" optional="true" label="number of abundant kmers required to discard a read" help="(default: 80% of the k-mers in a read)" />
93 </section> 94 </section>
94 <param argument="--max_k_freq" type="integer" value="20" label="number of times a kmer must occur to be considered abundant" />
95 <param argument="--min_lim" type="integer" value="" optional="true" label="number of rare kmers occuring in a row required to discard a read" help="(0/empty: 80% of the k-mer length)." />
96 <param argument="--max_lim" type="integer" value="" optional="true" label="number of abundant kmers required to discard a read" help="(0/empty: 80% of the k-mers in a read)" />
97 <section name="options_normalization" title="Normalization options" expanded="False"> 95 <section name="options_normalization" title="Normalization options" expanded="False">
98 <param argument="--normalize" type="integer" value="" label="normalize read depth according to k-mer coverage" /> 96 <param argument="--normalize" type="integer" value="" optional="true" label="normalize read depth according to k-mer coverage" />
99 </section> 97 </section>
100 <section name="options_kmer_char" title="Characterizing K-mers options" expanded="False"> 98 <section name="options_kmer_char" title="Characterizing K-mers options" expanded="False">
101 <param argument="--write_k_freq" type="boolean" checked="false" truevalue="--write_k_freq" falsevalue="" label="write kmers along with their frequency of occurrence and exit" /> 99 <param argument="--write_k_freq" type="boolean" checked="false" truevalue="--write_k_freq" falsevalue="" label="write kmers along with their frequency of occurrence and exit" />
102 <param argument="--k_dist" type="boolean" checked="false" truevalue="--k_dist" falsevalue="" label="print k-mer frequency distribution and exit" /> 100 <param argument="--k_dist" type="boolean" checked="false" truevalue="--k_dist" falsevalue="" label="print k-mer frequency distribution and exit" />
103 </section> 101 </section>
104 <section name="options_advanced_input" title="Advanced input options" expanded="False"> 102 <!--<section name="options_advanced_input" title="Advanced input options" expanded="False">
105 <param argument="--read_k_freq" type="boolean" checked="false" truevalue="--read_k_freq" falsevalue="" label="read a set of kmers along with their frequencies of occurrence instead of reading raw input files" /> 103 <param argument="\-\-read_k_freq" type="boolean" checked="false" truevalue="\-\-read_k_freq" falsevalue="" label="read a set of kmers along with their frequencies of occurrence instead of reading raw input files" />
106 </section> 104 </section>-->
107 </inputs> 105 </inputs>
108 <outputs> 106 <outputs>
109 <data format="fastqsanger.gz" name="clean" from_work_dir="clone_outputs/R1.fq.gz" label="${tool.name} on ${on_string}"> 107 <data format="fastqsanger.gz" name="clean" from_work_dir="clone_outputs/R1.fq.gz" label="${tool.name} on ${on_string}">
110 <filter>data_type['dt_select'] == 'single'</filter> 108 <filter>data_type['dt_select'] == 'single' and not options_kmer_char['k_dist']</filter>
111 </data> 109 </data>
112 110
113 <data format="fastqsanger.gz" name="clean_fwd" from_work_dir="clone_outputs/R1.1.fq.gz" label="${tool.name} on ${on_string} Forward reads"> 111 <data format="fastqsanger.gz" name="clean_fwd" from_work_dir="clone_outputs/R1.1.fq.gz" label="${tool.name} on ${on_string} Forward reads">
114 <filter>data_type['dt_select'] == 'pair'</filter> 112 <filter>data_type['dt_select'] == 'pair' and not options_kmer_char['k_dist']</filter>
115 </data> 113 </data>
116 <data format="fastqsanger.gz" name="clean_rev" from_work_dir="clone_outputs/R2.2.fq.gz" label="${tool.name} on ${on_string} Reverse reads"> 114 <data format="fastqsanger.gz" name="clean_rev" from_work_dir="clone_outputs/R2.2.fq.gz" label="${tool.name} on ${on_string} Reverse reads">
117 <filter>data_type['dt_select'] == 'pair'</filter> 115 <filter>data_type['dt_select'] == 'pair'</filter>
116 </data>
117 <data format="tabular" name="kfreq" label="${tool.name} on ${on_string} kmer frequencies">
118 <filter>options_kmer_char['write_k_freq']</filter>
119 </data>
120 <data format="tabular" name="kfreqdist" label="${tool.name} on ${on_string} kmer frequency distribution">
121 <filter>options_kmer_char['k_dist']</filter>
118 </data> 122 </data>
119 </outputs> 123 </outputs>
120 <tests> 124 <tests>
121 <test> 125 <test>
122 <conditional name="data_type"> 126 <conditional name="data_type">
123 <param name="dt_select" value="single" /> 127 <param name="dt_select" value="single" />
124 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> 128 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
125 </conditional> 129 </conditional>
126 <param name="oligo_len_1" value="6" />
127 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> 130 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
131 </test>
132 <test>
133 <conditional name="data_type">
134 <param name="dt_select" value="single" />
135 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
136 </conditional>
137 <section name="options_kmer_char">
138 <param name="write_k_freq" value="--write_k_freq" />
139 </section>
140 <output name="kfreq" file="kmerfilter/kfreq.tsv"/>
128 </test> 141 </test>
129 <!--<test> 142 <!--<test>
130 <conditional name="data_type"> 143 <conditional name="data_type">
131 <param name="dt_select" value="single" /> 144 <param name="dt_select" value="single" />
132 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> 145 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />