Mercurial > repos > iuc > srst2

annotate srst2.xml @ 2:1f1738444233 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
author iuc
date Mon, 28 Oct 2024 13:08:41 +0000
parents 4e0b819bf73e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
1 <tool id="srst2" name="SRST2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
2 <description>Short Read Sequence Typing for Bacterial Pathogens</description>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
3 <macros>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
4 <import>macros.xml</import>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
5 <token name="@FAST_A_Q_FORMATS@">fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
6 </macros>
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
7 <expand macro="xrefs"/>
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
8 <expand macro="requirements"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
9 <version_command>srst2 --version</version_command>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
11 #if $input.selector == "single"
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
12 #set ext=$input.single_input.datatype.file_ext
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
13 ln -s $input.single_input './input_read1.$ext' &&
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
14 #else if $input.selector == "paired"
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
15 #set ext_1=$input.paired_input1.datatype.file_ext
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
16 #set ext_2=$input.paired_input2.datatype.file_ext
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
17 ln -s $input.paired_input1 './input_read1.$ext_1' &&
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
18 ln -s $input.paired_input2 './input_read2.$ext_2' &&
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
19 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
20 #for $i, $s in enumerate($prev_output)
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
21 #if $s
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
22 ln -s $s './$i-prev_output.txt' &&
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
23 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
24 #end for
1
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
25 #if $use_gene_db.selector == "yes"
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
26 #for $i, $s in enumerate($use_gene_db.gene_db)
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
27 #if $s
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
28 ln -s $s './$i-gene_db.fasta' &&
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
29 #end if
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
30 #end for
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
31 #end if
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
32 #if $use_mlst_db.selector == "yes"
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
33 #set ext_3=$use_mlst_db.mlst_definitions.datatype.file_ext
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
34 ln -s $use_mlst_db.mlst_db './mlst_db.fasta' &&
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
35 ln -s $use_mlst_db.mlst_definitions './mlst_definitions.$ext_3' &&
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
36 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
37 srst2
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
38 #if $input.selector == "single"
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
39 --input_se './input_read1.$ext'
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
40 --read_type ${input.read_type}
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
41 #else if $input.selector == "paired"
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
42 --input_pe './input_read1.$ext_1' './input_read2.$ext_2'
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
43 $input.merge_paired
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
44 --forward _read1
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
45 --reverse _read2
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
46 --read_type ${input.read_type}
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
47 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
48 #if $use_mlst_db.selector == "yes"
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
49 --mlst_db './mlst_db.fasta'
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
50 --mlst_definitions './mlst_definitions.$ext_3'
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
51 --mlst_delimiter '$use_mlst_db.mlst_delimiter'
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
52 --mlst_max_mismatch $use_mlst_db.mlst_max_mismatch
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
53 --min_depth $use_mlst_db.min_depth
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
54 --min_edge_depth $use_mlst_db.min_edge_depth
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
55 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
56 #if $use_gene_db.selector == "yes"
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
57 --gene_db
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
58 #for $i, $s in enumerate($use_gene_db.gene_db)
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
59 #if $s
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
60 '$i-gene_db.fasta'
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
61 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
62 #end for
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
63 $use_gene_db.no_gene_details
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
64 --gene_max_mismatch $use_gene_db.gene_max_mismatch
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
65 --min_coverage $use_gene_db.min_coverage
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
66 --max_divergence $use_gene_db.max_divergence
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
67 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
68 --prob_err $prob_err
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
69 #if $truncation_score_tolerance
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
70 --truncation_score_tolerance $truncation_score_tolerance
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
71 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
72 #if $stop_after
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
73 --stop_after $stop_after
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
74 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
75 --max_unaligned_overlap $max_unaligned_overlap
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
76 --mapq $mapq
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
77 --baseq $baseq
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
78 --output 'output'
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
79 #if $prev_output
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
80 --prev_output
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
81 #for $i, $s in enumerate($prev_output)
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
82 #if $s
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
83 '$i-prev_output.txt'
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
84 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
85 #end for
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
86 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
87 #if 'log' in str($output_files_selector)
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
88 --log
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
89 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
90 #if 'save_scores' in str($output_files_selector)
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
91 --save_scores
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
92 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
93 #if 'report_new_consensus' in str($output_files_selector)
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
94 --report_new_consensus
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
95 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
96 #if 'report_all_consensus' in str($output_files_selector)
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
97 --report_all_consensus
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
98 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
99 #if 'keep_interim_alignment' in str($output_files_selector)
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
100 --keep_interim_alignment
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
101 #end if
1
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
102 ## |true here is added in order not to search for a file that is not produced at all, such that if the user provided no gene/MLST databases or there are no outputs found, the tool will run successfully and only notify the user that no outputs are found
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
103 #if 'report_new_consensus' in str($output_files_selector) and $use_gene_db.selector == "yes" and $use_mlst_db.selector == "yes"
1
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
104 && mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput | true
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
105 #end if
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
106
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
107 #if $use_gene_db.selector == "yes" and $use_gene_db.no_gene_details
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
108 && mkdir -p geneTypingOutput/ geneTypingOutputFull/ && cp output__genes__*__results.txt geneTypingOutput | true && cp output__fullgenes__*__results.txt geneTypingOutputFull | true
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
109 #end if
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
110
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
111 #if 'save_scores' in str($output_files_selector)
1
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
112 && mkdir -p scoresOutput/ && cp *.scores scoresOutput | true
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
113 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
114 #if $input.selector == "single" or $input.selector == "paired"
1
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
115 && mkdir -p bowtie2Alignments/ && cp *.sorted.bam bowtie2Alignments | true
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
116 && mkdir -p samtoolsPileup/ && cp output__input.*.pileup samtoolsPileup | true
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
117 #end if
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
118 ]]></command>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
119 <inputs>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
120 <conditional name="input">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
121 <param name="selector" type="select" label="Reads files type for anaylsis">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
122 <option value="single">Single-end</option>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
123 <option value="paired">Paired-end</option>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
124 <option value="only_compiling_previous_results">Only Compiling Previous SRST2 Results</option>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
125 </param>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
126 <when value="single">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
127 <param name="single_input" type="data" format="@FAST_A_Q_FORMATS@" label="Single end read file(s) for analysing (may be gzipped)"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
128 <expand macro="read_type_options" />
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
129 </when>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
130 <when value="paired">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
131 <param name="paired_input1" type="data" format="@FAST_A_Q_FORMATS@" label="Paired end read files for analysing (may be gzipped)"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
132 <param name="paired_input2" type="data" format="@FAST_A_Q_FORMATS@" label="Paired end read files for analysing (may be gzipped)"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
133 <param argument="--merge_paired" type="boolean" truevalue="--merge_paired" falsevalue="" checked="false" label="Do you want to merge the data to get a single result" help="Important only if all the input read sets belong to a single sample"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
134 <expand macro="read_type_options" />
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
135 </when>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
136 <when value="only_compiling_previous_results">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
137 </when>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
138 </conditional>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
139 <conditional name="use_mlst_db">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
140 <param name="selector" type="select" label="Do you want to provide an MLST database of all allele sequences for the MLST scheme?">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
141 <option value="yes">Yes</option>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
142 <option value="no">No</option>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
143 </param>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
144 <when value="yes">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
145 <param argument="--mlst_db" type="data" format="fasta" label="Fasta file of MLST alleles"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
146 <param argument="--mlst_definitions" type="data" format="tabular" label="ST definitions for MLST scheme" help="This is the file that tells you the ST number that is assigned to known combinations of alleles. Column 1 is the ST, and subsequent columns are the loci that make up the scheme."/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
147 <param argument="--mlst_delimiter" type="text" value="-" label="Character(s) separating gene name from allele number in MLST database" help="E.g.'-', as in arcc-1">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
148 <sanitizer invalid_char="">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
149 <valid initial="string.letters,string.digits">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
150 <add value="\" />
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
151 <add value="-" />
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
152 <add value="/" />
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
153 <add value="+" />
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
154 <add value="=" />
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
155 <add value=" " />
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
156 <add value="_" />
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
157 </valid>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
158 </sanitizer>
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
159 <validator type="regex">[A-Za-z0-9 =_/+-]+</validator>
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
160 </param>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
161 <param argument="--mlst_max_mismatch" type="integer" value="10" label="Maximum number of mismatches per read for MLST allele calling"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
162 <param argument="--min_depth" type="integer" value="5" label="Minimum mean depth to flag as dubious allele call"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
163 <param argument="--min_edge_depth" type="integer" value="2" label="Minimum edge depth to flag as dubious allele call"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
164 </when>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
165 <when value="no">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
166 </when>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
167 </conditional>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
168 <conditional name="use_gene_db">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
169 <param name="selector" type="select" label="Do you want to use a Gene database(s)?">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
170 <option value="yes">Yes</option>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
171 <option value="no">No</option>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
172 </param>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
173 <when value="yes">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
174 <param argument="--gene_db" type="data" optional="true" multiple="true" format="fasta" label="Gene database(s)" help="Fasta file/s for gene databases"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
175 <param argument="--no_gene_details" type="boolean" truevalue="" falsevalue="--no_gene_details" checked="false" label="Do you want reporting of gene typing?"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
176 <param argument="--gene_max_mismatch" type="integer" value="10" label="Maximum number of mismatches per read for gene detection and allele calling"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
177 <param argument="--min_coverage" type="integer" value="90" label="Minimum %coverage cutoff for gene reporting"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
178 <param argument="--max_divergence" type="integer" value="10" label="Maximum %divergence cutoff for gene reporting"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
179 </when>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
180 <when value="no">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
181 </when>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
182 </conditional>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
183 <param name="output_files_selector" type="select" label="Select all outputs you need" multiple="true">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
184 <option value="log">Save the log</option>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
185 <option value="save_scores">Report scores</option>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
186 <option value="report_new_consensus">Report the consensus allele if a matching alleles is not found</option>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
187 <option value="report_all_consensus">Report the consensus allele for the most likely allele</option>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
188 <option value="keep_interim_alignment">Keep interim files (sam and unsorted bam)</option>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
189 </param>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
190 <param argument="--prob_err" type="float" min="0" max="1" value="0.01" label="Probability of sequencing error"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
191 <param argument="--truncation_score_tolerance" optional="true" type="float" label="% increase in score allowed to choose non-truncated allele"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
192 <param argument="--stop_after" type="integer" optional="true" label="Stop mapping after this number of reads have been mapped" help="Leave empty to map all"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
193 <param argument="--max_unaligned_overlap" type="integer" value="10" label="Read discarded from alignment" help="if either of its ends has unaligned overlap with the reference that is longer than this value"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
194 <param argument="--mapq" type="integer" value="1" label="Samtools -q parameter (Minimum mapping quality)"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
195 <param argument="--baseq" type="integer" value="20" label="Samtools -Q parameter (Minimum base quality)"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
196 <param argument="--prev_output" type="data" format="tabular" multiple="true" optional="true" label="SRST2 results files to compile" help="Any new results from this run will also be incorporated"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
197 </inputs>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
198 <outputs>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
199 <data name="mlst_results" format="tabular" from_work_dir="output__mlst__mlst_db__results.txt" label="${tool.name} on ${on_string}: MLST Results">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
200 <filter>use_mlst_db['selector'] == "yes"</filter>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
201 </data>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
202 <collection name="gene_typing" type="list" label="${tool.name} on ${on_string}: Gene typing results files" >
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
203 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutput" format="tabular"/>
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
204 <filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter>
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
205 </collection>
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
206 <collection name="gene_typing_full" type="list" label="${tool.name} on ${on_string}: Full Gene typing results files" >
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
207 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="geneTypingOutputFull" format="tabular"/>
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
208 <filter>use_gene_db['selector'] == "yes" and use_gene_db['no_gene_details'] is True</filter>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
209 </collection>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
210 <data name="Compiled_gene_and_mlst_output" format="tabular" from_work_dir="output__compiledResults.txt" label="${tool.name} on ${on_string}: Compiled MLST and Gene databases Results">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
211 </data>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
212 <data name="all_consensus" format="fasta" from_work_dir="output.all_consensus_alleles.fasta" label="${tool.name} on ${on_string}: All consensus Results">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
213 <filter>"report_all_consensus" in output_files_selector</filter>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
214 </data>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
215 <collection name="new_consensus" type="list" label="${tool.name} on ${on_string}: New consensus Results" >
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
216 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="allelesOutput" format="pileup"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
217 <filter>"report_new_consensus" in output_files_selector</filter>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
218 </collection>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
219 <collection name="scores_ofEachAllele" type="list" label="${tool.name} on ${on_string}: Scores for each allele in the database(s)" >
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
220 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="scoresOutput" format="tabular"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
221 <filter>"save_scores" in output_files_selector</filter>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
222 </collection>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
223 <collection name="bowtie2_alignment_output" type="list" label="${tool.name} on ${on_string}: Bowtie2 alignment of reads to each input database" >
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
224 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="bowtie2Alignments" format="bam"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
225 <filter>input['selector'] == "single" or input['selector'] == "paired"</filter>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
226 </collection>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
227 <collection name="samtools_pileup_alignment" type="list" label="${tool.name} on ${on_string}: Samtools pileup of the alignment to each input database" >
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
228 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="samtoolsPileup" format="pileup"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
229 <filter>input['selector'] == "single" or input['selector'] == "paired"</filter>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
230 </collection>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
231 <data name="log_output" format="tabular" from_work_dir="output.log" label="${tool.name} on ${on_string}: Log file">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
232 <filter>"log" in output_files_selector</filter>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
233 </data>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
234 </outputs>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
235 <tests>
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
236 <test expect_num_outputs="10">
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
237 <param name="prob_err" value="0.01"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
238 <param name="max_unaligned_overlap" value="10"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
239 <param name="mapq" value="1"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
240 <param name="baseq" value="20"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
241 <param name="output_files_selector" value="log,save_scores,report_new_consensus,report_all_consensus"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
242 <conditional name="input">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
243 <param name="selector" value="paired"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
244 <param name="paired_input1" value="ERR024070_1_reduced_forward_reads.fastqsanger.gz"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
245 <param name="paired_input2" value="ERR024070_2_reduced_reverse_reads.fastqsanger.gz"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
246 <param name="merge_paired" value="false"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
247 <param name="read_type" value="q"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
248 </conditional>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
249 <conditional name="use_mlst_db">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
250 <param name="selector" value="yes"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
251 <param name="mlst_db" value="Escherichia_coli1R.fasta"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
252 <param name="mlst_definitions" value="profiles_csv"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
253 <param name="mlst_delimiter" value="_"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
254 <param name="mlst_max_mismatch" value="10"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
255 <param name="min_depth" value="5"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
256 <param name="min_edge_depth" value="2"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
257 </conditional>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
258 <conditional name="use_gene_db">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
259 <param name="selector" value="yes"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
260 <param name="gene_db" value="ARGannotR.fasta"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
261 <param name="no_gene_details" value="true"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
262 <param name="gene_max_mismatch" value="10"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
263 <param name="min_coverage" value="90"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
264 <param name="max_divergence" value="10"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
265 </conditional>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
266 <output name="mlst_results">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
267 <assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
268 <has_text text="fumC"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
269 <has_n_lines n="2"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
270 </assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
271 </output>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
272 <output_collection name="gene_typing" type="list">
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
273 <element name="output__genes__0-gene_db__results.txt">
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
274 <assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
275 <has_text text="AmpC1_Ecoli_Bla"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
276 <has_n_lines n="2"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
277 </assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
278 </element>
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
279 </output_collection>
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
280 <output_collection name="gene_typing_full" type="list">
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
281 <element name="output__fullgenes__0-gene_db__results.txt">
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
282 <assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
283 <has_text text="AmpC1_Ecoli_Bla"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
284 <has_n_lines n="2"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
285 </assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
286 </element>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
287 </output_collection>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
288 <output name="Compiled_gene_and_mlst_output">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
289 <assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
290 <has_text text="fumC"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
291 <has_n_lines n="2"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
292 </assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
293 </output>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
294 <output name="all_consensus">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
295 <assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
296 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
297 <has_n_lines n="2"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
298 </assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
299 </output>
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
300 <output_collection name="new_consensus" type="list" count="1">
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
301 <element name="49__AmpC1_Ecoli_Bla__AmpC1__1670.output__input.0-gene_db.pileup">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
302 <assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
303 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
304 <has_n_lines n="1196"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
305 </assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
306 </element>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
307 </output_collection>
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
308 <output_collection name="samtools_pileup_alignment" type="list" count="1">
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
309 <element name="output__input.0-gene_db.pileup">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
310 <assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
311 <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
312 <has_n_lines n="1196"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
313 </assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
314 </element>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
315 </output_collection>
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
316 <output_collection name="bowtie2_alignment_output" type="list" count="1">
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
317 <element name="output__input.0-gene_db.sorted.bam">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
318 <assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
319 <has_size value="18500" delta="1000"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
320 </assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
321 </element>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
322 </output_collection>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
323 <output name="log_output">
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
324 <assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
325 <has_text text="Building"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
326 <has_n_lines n="52"/>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
327 </assert_contents>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
328 </output>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
329 </test>
1
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
330 <test expect_num_outputs="7">
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
331 <param name="prob_err" value="0.01"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
332 <param name="max_unaligned_overlap" value="10"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
333 <param name="mapq" value="1"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
334 <param name="baseq" value="20"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
335 <param name="output_files_selector" value="log,save_scores,report_new_consensus,report_all_consensus"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
336 <conditional name="input">
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
337 <param name="selector" value="paired"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
338 <param name="paired_input1" value="ERR024070_1_reduced_forward_reads.fastqsanger.gz"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
339 <param name="paired_input2" value="ERR024070_2_reduced_reverse_reads.fastqsanger.gz"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
340 <param name="merge_paired" value="false"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
341 <param name="read_type" value="q"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
342 </conditional>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
343 <conditional name="use_mlst_db">
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
344 <param name="selector" value="no"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
345 </conditional>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
346 <conditional name="use_gene_db">
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
347 <param name="selector" value="no"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
348 </conditional>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
349 <output name="Compiled_gene_and_mlst_output">
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
350 <assert_contents>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
351 <has_n_lines n="0"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
352 </assert_contents>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
353 </output>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
354 <output name="all_consensus">
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
355 <assert_contents>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
356 <has_size value="0" delta="0"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
357 </assert_contents>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
358 </output>
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
359 <output_collection name="new_consensus" type="list" count="0"/>
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
360 <output_collection name="samtools_pileup_alignment" type="list" count="0"/>
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
361 <output_collection name="bowtie2_alignment_output" type="list" count="0"/>
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
362 <output_collection name="scores_ofEachAllele" type="list" count="0"/>
1
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
363 <output name="log_output">
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
364 <assert_contents>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
365 <has_text text="Total paired readsets found:1"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
366 <has_n_lines n="4"/>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
367 </assert_contents>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
368 </output>
4e0b819bf73e planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5
iuc
parents: 0
diff changeset
369 </test>
0
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
370 </tests>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
371 <help><![CDATA[
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
372 SRST2
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
373 =====
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
374 Short Read Sequence Typing for Bacterial Pathogens
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
375
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
376 This program is designed to take Illumina sequence data, a MLST (Multi Locus Sequence Types) database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs (Serotypes) and/or reference genes
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
377
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
378 Read more about the tool: https://holtlab.net/2014/12/27/behind-the-paper-srst2-for-short-read-sequence-typing-of-bacterial-pathogens/
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
379
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
380 Input
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
381 =====
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
382 Learn more about all inputs and their formates: https://github.com/katholt/srst2#input-read-formats-and-options
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
383
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
384 Output
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
385 ======
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
386 Learn more about all outputs: https://github.com/katholt/srst2#output-files
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
387 ]]></help>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
388 <citations>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
389 <citation type="doi">10.1186/s13073-014-0090-6</citation>
36f105850c0d planemo upload for repository https://github.com/katholt/srst2 commit 00fa01604956cb2e175fe9df199fc98956efad27
iuc
parents:
diff changeset
390 </citations>
2
1f1738444233 planemo upload for repository https://github.com/katholt/srst2 commit 90275e51aa271edacdd9d277c441e38e99502c53
iuc
parents: 1
diff changeset
391 </tool>