Mercurial > repos > estrain > seqsero2_v1_0_1

comparison seqsero2.xml @ 41:526617c6f359

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author estrain
date Sat, 07 Sep 2019 19:47:49 -0400
parents 3eaa774bc1ee
children
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40:f918518b7d7b 41:526617c6f359
16 16
17 #if $reads.reads_select == 'history' 17 #if $reads.reads_select == 'history'
18 #set $name = $reads.forward.name.split('.')[0].replace(' ','_') 18 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
19 #set $forward = $reads.forward 19 #set $forward = $reads.forward
20 #set $reverse = $reads.reverse 20 #set $reverse = $reads.reverse
21 #else 21 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
22 #set $tval = 2
23 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
24 gunzip -c $reverse > reverse.fastq;
25 #set $reverse = './reverse.fastq'
26 gunzip -c $forward > forward.fastq;
27 #set $forward = './forward.fastq'
28 #end if
29 ln -s $forward ${name}_1.fastq;
30 ln -s $reverse ${name}_2.fastq;
31 #else if $reads.reads_select == 'collection'
22 #set $name = $reads.coll.name.replace(' ', '_') 32 #set $name = $reads.coll.name.replace(' ', '_')
23 #set $forward = $reads.coll.forward 33 #set $forward = $reads.coll.forward
24 #set $reverse = $reads.coll.reverse 34 #set $reverse = $reads.coll.reverse
35 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
36 #set $tval = 2
37 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
38 gunzip -c $reverse > reverse.fastq;
39 #set $reverse = './reverse.fastq'
40 gunzip -c $forward > forward.fastq;
41 #set $forward = './forward.fastq'
42 #end if
43 ln -s $forward ${name}_1.fastq;
44 ln -s $reverse ${name}_2.fastq;
45 #else
46 #set $name = $reads.assembly.name.replace(' ', '_')
47 #set $ga = $reads.assembly
48 #set $infile = $name + ".fasta"
49 ln -s $ga ${name}.fasta;
50 #set $tval = 4
51 #set $mode='k'
25 #end if 52 #end if
26 echo $name ; 53 echo $name ;
27 echo "-=-=-=-=-" ; 54 echo "-=-=-=-=-" ;
28 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
29 gunzip -c $forward > forward.fastq;
30 #set $forward = './forward.fastq'
31 #end if
32 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
33 gunzip -c $reverse > reverse.fastq;
34 #set $reverse = './reverse.fastq'
35 #end if
36 ln -s $forward ${name}_1.fastq;
37 ln -s $reverse ${name}_2.fastq;
38 touch output/SeqSero_log.txt ; 55 touch output/SeqSero_log.txt ;
39 python $__tool_directory__/SeqSero2_package.py 56 python $__tool_directory__/SeqSero2_package.py
40 -p \${GALAXY_SLOTS:-4} 57 -p \${GALAXY_SLOTS:-4}
41 -t 2 58 -t $tval
42 -m $mode 59 -m $mode
43 -d ./output 60 -d ./output
44 #if $mode == 'a': 61 #if $mode == 'a':
45 -b $maptype 62 -b $maptype
46 #end if 63 #end if
47 -i ${name}_1.fastq ${name}_2.fastq && 64 -i $infile &&
48 echo "-=-=-=-=-" && 65 echo "-=-=-=-=-" &&
49 cat output/SeqSero_log.txt && 66 cat output/SeqSero_log.txt &&
50 echo "-=-=-=-=-" && 67 echo "-=-=-=-=-" &&
51 ls -lah ./output 68 ls -lah ./output
52 ]]></command> 69 ]]></command>
53 <inputs> 70 <inputs>
54 71
55 <conditional name="reads"> 72 <conditional name="reads">
56 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history"> 73 <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
57 <option value="collection">Paired collection from your history</option> 74 <option value="collection">Paired collection from your history</option>
58 <option value="history">Two FASTQ datasets from your history</option> 75 <option value="history">Two FASTQ datasets from your history</option>
76 <option value="genome">Genome Assembly</option>
59 </param> 77 </param>
60 <when value="collection"> 78 <when value="collection">
61 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" /> 79 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
62 </when> 80 </when>
63 <when value="history"> 81 <when value="history">
64 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" /> 82 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
65 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" /> 83 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
84 </when>
85 <when value="genome">
86 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
66 </when> 87 </when>
67 </conditional> 88 </conditional>
68 89
69 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" /> 90 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
70 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> --> 91 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
75 <option value="4">4</option> --> 96 <option value="4">4</option> -->
76 <!-- </param> --> 97 <!-- </param> -->
77 98
78 <param label="Analysis mode" type="select" name="mode"> 99 <param label="Analysis mode" type="select" name="mode">
79 <option value="a">allele mode</option> 100 <option value="a">allele mode</option>
80 <option value="k">k-mer mode</option> 101 <option value="k">k-mer mode</option>
81 </param> 102 </param>
82 103
83 <param name="maptype" type="select" label="Algorithms for BWA mapping"> 104 <param name="maptype" type="select" label="Algorithms for BWA mapping">
84 <option value="mem">mem</option> 105 <option value="mem">mem</option>
85 <option value="sam">sam</option> 106 <option value="sam">sam</option>