annotate rna_quast.xml @ 8:f73ab5187eed draft default tip

planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 140ef122cde10b77c9c9466cf8464c1bce6599e9
author iuc
date Fri, 30 Aug 2024 14:12:04 +0000
parents 3125faf00ffd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
1 <tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
2 <description>A quality assessment tool for De Novo transcriptome assemblies</description>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
3 <macros>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
4 <import>macros.xml</import>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
5 </macros>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
6 <expand macro='xrefs'/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
7 <expand macro='requirements'/>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
8 <stdio>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
9 <regex match="Traceback " source="both" level="fatal" description="rnaQuast failed" />
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
10 </stdio>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
12 mkdir -p './complete_reports/' &&
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
13 mkdir -p './fasta_files/' &&
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
14 #import os, re, glob
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
15 #for $i in $transcripts
7
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
16 ln -s '$i' '${re.sub('[^\w.]', '_', i.element_identifier)}' &&
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
17 #end for
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
18 #if $reference
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
19 #for $rf in $reference
7
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
20 ln -s '$rf' '${re.sub('[^\w.]', '_', rf.element_identifier)}' &&
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
21 #end for
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
22 #end if
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
23 #if $gene_coordinates.selector == "true"
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
24 #for $g in $gene_coordinates.gtf
7
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
25 ln -s '$g' '${re.sub('[^\w.]', '_', g.element_identifier)}' &&
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
26 #end for
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
27 #end if
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
28 mkdir outputdir &&
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
29 rnaQUAST.py
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
30 --threads \${GALAXY_SLOTS:-8}
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
31 --transcripts
3
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
32 #for $i in $transcripts
7
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
33 '${re.sub('[^\w.]', '_', i.element_identifier)}'
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
34 #end for
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
35 #if $reads_option.selector == 'paired'
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
36 --left_reads '${reads_option.forward_reads}'
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
37 --right_reads '${reads_option.reverse_reads}'
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
38 #else if $reads_option.selector == 'single'
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
39 --single_reads '${reads_option.single_reads}'
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
40 #end if
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
41 $advanced_options.strand_specific
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
42 #if $reads_alignment
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
43 --reads_alignment '${reads_alignment}'
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
44 #end if
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
45 #if $reference
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
46 -r
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
47 #for $rf in $reference
7
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
48 '${re.sub('[^\w.]', '_', rf.element_identifier)}'
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
49 #end for
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
50 #end if
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
51 #if $gene_coordinates.selector == "true"
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
52 --gtf
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
53 #for $g in $gene_coordinates.gtf
7
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
54 '${re.sub('[^\w.]', '_', g.element_identifier)}'
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
55 #end for
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
56 $gene_coordinates.disable_infer_genes
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
57 $gene_coordinates.disable_infer_transcripts
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
58 #end if
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
59 $advanced_options.prokaryote
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
60 --min_alignment $advanced_options.min_alignment
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
61 $advanced_options.blat
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
62
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
63 #if "pdf" not in $output_options.out_sr
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
64 --no_plots
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
65 #end if
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
66 #if $use_busco.selector == 'true'
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
67 --busco
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
68 #if $use_busco.lineage_conditional.selector == 'cached':
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
69 '${use_busco.lineage_conditional.cached_db.fields.path}'
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
70 #else
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
71 $use_busco.lineage
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
72 #end if
3
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
73 #end if
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
74 ## $advanced_options.gene_mark
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
75 $advanced_options.meta
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
76 --lower_threshold $advanced_options.lower_threshold
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
77 --upper_threshold $advanced_options.upper_threshold
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
78 -o outputdir
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
79
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
80 #if 'gz' in $output_options.out_add
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
81 && tar -czvf results.tar.gz './outputdir'
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
82 #end if
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
83
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
84 #if len($transcripts) == 1
7
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
85 #set $path = "/".join(['outputdir',re.sub('[^\w.]', '_', $transcripts[0].element_identifier).split(".")[0]]) + "_output"
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
86 && mv '${path}' './results'
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
87 ## rename .list files to .txt files to make them detectable
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
88 && find './results/' -name "*.list" -exec mv {} {}.txt \;
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
89 && true
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
90 && printf "************ METRICS/TRANSCRIPTS ***************\n" > stats.txt
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
91 && for file_name in ./results/*txt; do printf "\n************ \$file_name ************\n" >> stats.txt
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
92 && sed 's/^ ==.*/&\n/' \$file_name | tail -q -n +2 "\$file_name" >> stats.txt;
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
93 done
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
94 && cat stats.txt > $stats
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
95 #if $gene_coordinates.selector == 'true' and $reference
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
96 && mv ./results/*fasta ./fasta_files/
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
97 #end if
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
98 #else
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
99 && mkdir -p './results/'
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
100 #if $gene_coordinates.selector == 'true' and $reference
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
101 #for $i, $transcript in enumerate($transcripts)
7
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
102 #set $path = "/".join(['outputdir',re.sub('[^\w.]', '_', $transcripts[$i].element_identifier).split(".")[0]]) + "_output"
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
103 && rm -r ./results
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
104 && cp -r $path './results'
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
105 && mv ./results/*fasta './fasta_files/'
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
106 #end for
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
107 #end if
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
108 && find './outputdir/comparison_output' -name "*.list" -exec mv {} {}.txt \;
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
109 && true
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
110 && printf "************ COMPARISON METRICS ***************\n" > stats.txt
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
111 && for file_name in ./outputdir/comparison_output/*txt; do printf "\n************ \$file_name ************\n" >> stats.txt
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
112 && sed 's/^ ==.*/&\n/' \$file_name | tail -q -n +2 "\$file_name" >> stats.txt; done
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
113 && cat stats.txt > $stats
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
114 #end if
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
115 ]]> </command>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
116 <inputs>
3
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
117 <param argument="--transcripts" type="data" format="fasta" multiple="true" label="Transcripts" help="File(s) with transcripts in FASTA format."/>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
118 <conditional name="reads_option">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
119 <param name="selector" type="select" label="Single-end or paired-end reads">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
120 <option value="" selected="true">Disabled-end</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
121 <option value="single" selected="true">Single-end</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
122 <option value="paired">Paired-end (as individual datasets)</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
123 </param>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
124 <when value=""/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
125 <when value="single">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
126 <param format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" name="single_reads" type="data" label="RNA-Seq FASTQ/FASTA file"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
127 </when>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
128 <when value="paired">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
129 <param name="forward_reads" format="fastq,fastq.gz,fastqsanger ,fastqsanger.gz" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
130 <param name="reverse_reads" format="fastq,fastq.gz,fastqsanger, fastqsanger.gz" type="data" label="RNA-Seq FASTQ/FASTA file, reverse reads"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
131 </when>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
132 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
133 <param argument="--reference" type="data" format="fasta" label="Reference genome" multiple="true" optional="true" help="File with reference genome containing all chromosomes/scaffolds in FASTA forma." />
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
134 <conditional name="gene_coordinates">
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
135 <param name="selector" type="select" label="Genome annotation" help="Genome annotation file. We recommend to use files downloaded from GENCODE or Ensembl.">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
136 <option value="true">Enabled</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
137 <option value="false" selected="true">Disabled</option>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
138 </param>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
139 <when value="true">
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
140 <param argument="--gtf" type="data" format="gtf,gff,gff3" multiple="true" label="GTF/GFF file" />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
141 <param argument="--disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="false" label=" Disable infer genes"
3
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
142 help="Use this option if your GTF file already contains genes records, otherwise gffutils will fix it. Note that gffutils may work for quite a long time"/>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
143 <param argument="--disable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="false" label="Disable infer transcripts" help="Is option if your GTF file already contains transcripts records, otherwise gffutils will fix it."/>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
144 </when>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
145 <when value="false">
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
146 </when>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
147 </conditional>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
148 <param argument="--reads_alignment" type="data" format="sam" label="Aligned reads to reference genome" optional="true" help="File with read alignments to the reference genome" />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
149 <conditional name="use_busco">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
150 <param argument="selector" type="select" label="Run BUSCO" help="BUSCO allows to detect core genes in the assembled transcripts">
3
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
151 <option value="false">Disabled</option>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
152 <option value="true">Enabled</option>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
153 </param>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
154 <when value="false"/>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
155 <when value="true">
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
156 <conditional name="lineage_conditional">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
157 <param name="selector" type="select" label="Lineage data source">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
158 <option value="download">Download lineage data</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
159 <option value="cached" selected="true">Use cached lineage data</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
160 </param>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
161 <when value="cached">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
162 <param name="cached_db" label="Cached database with lineage" type="select">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
163 <options from_data_table="busco_database">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
164 <validator message="No BUSCO database is available" type="no_options" />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
165 </options>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
166 </param>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
167 </when>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
168 <when value="download">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
169 <param name="lineage" type="select" label="Lineage" help="Select a lineage for using BUSCO">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
170 <option value="metazoa">Metazoa</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
171 <option value="eukaryota">Eukaryota</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
172 <option value="arthropoda">Arthropoda</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
173 <option value="vertebrata">Vertebrata</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
174 <option value="fungi">Fungi</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
175 <option value="bacteria">Bacteria</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
176 </param>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
177 </when>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
178 </conditional>
3
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
179 </when>
a9edbe21bf47 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 5ba8cddaafd411e30baa19da0f93959ef5ccaca0"
iuc
parents: 2
diff changeset
180 </conditional>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
181 <section name="advanced_options" title="Advaced options" >
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
182 <param name="strand_specific" argument="-ss" type="boolean" truevalue="-ss" falsevalue="" checked="false" label="Strand-specific RNA-seq data"
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
183 help="Set if transcripts were assembled using strand-specific RNA-Seq data in order to benefit from knowing whether the transcript originated from the + or - strand"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
184 <param argument="--min_alignment" type="integer" min="0" value="50" label="Minimal alignment length to be used" help="Default value is 50"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
185 <param argument="--blat" type="boolean" truevalue="--blat" falsevalue="" checked="false" label="Run with BLAT instead of GMAP" help="BALT is especially useful for aligning long sequences and gapped mapping, which cannot be performed properly by other fast sequence mappers designed for short reads. " />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
186 <!-- GeneMarkST is not in Bioconda -->
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
187 <!--param argument="-\-gene_mark" type="boolean" truevalue="-\-gene_mark" falsevalue="" checked="false" label="Run with GeneMarkS-T gene prediction tool?"
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
188 help="GeneMarkS-T allows to predict genes in the assembled transcripts without reference genome"/-->
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
189 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Meta Transcriptome" help="Run quality asessment for meta-transcriptome assemblies" />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
190 <param argument="--lower_threshold" type="integer" value="50" label="Lower threshold for x-assembled/covered/matched metrics." />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
191 <param argument="--upper_threshold" type="integer" value="95" label="Upper threshold for x-assembled/covered/matched metrics." />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
192 <param argument="--prokaryote" type="boolean" truevalue="--prokaryote" falsevalue="" checked="false" label="Prokararyotic organism(s)" help="Use this option if the genome is prokaryotic"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
193 </section>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
194 <section name="output_options" title="Output options" expanded="true">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
195 <param name="out_sr" type="select" multiple="true" display="checkboxes" label="Short report formats">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
196 <option value="tabular">Tabular</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
197 <option value="tex">TeX</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
198 <option value="pdf" selected="true">PDF</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
199 </param>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
200 <param name="out_add" type="select" label="Additional outputs" multiple="true" display="checkboxes">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
201 <option value="complete">Complete report</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
202 <option value="fasta" >FASTA files</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
203 <option value="logs">Logs</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
204 <option value="gz">Compressed output folder</option>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
205 </param>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
206 </section>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
207 </inputs>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
208 <outputs>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
209 <data name="stats" format="txt" label="${tool.name} on ${on_string}: complete report">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
210 <filter>output_options['out_add'] and "complete" in output_options['out_add']</filter>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
211 </data>
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
212 <collection name="list_logs" type="list" label="${tool.name} on ${on_string}: logs">
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
213 <discover_datasets ext="txt" pattern="(?P&lt;name&gt;.+)\.log" directory="outputdir/logs" visible="false" />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
214 <filter>output_options['out_add'] and "logs" in output_options['out_add']</filter>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
215 </collection>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
216 <collection name="fasta_files" type="list" label="${tool.name} on ${on_string}: FASTA files">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
217 <discover_datasets ext="fasta" pattern="(?P&lt;name&gt;.+)\.fasta" directory="fasta_files" visible="false" />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
218 <filter>output_options['out_add'] and "fasta" in output_options['out_add']</filter>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
219 <filter>gene_coordinates['selector'] == 'true'</filter>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
220 <filter>reference</filter>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
221 </collection>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
222 <data name="compressed_files" format="tgz" label="${tool.name} on ${on_string}: compressed results folder" from_work_dir="results.tar.gz">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
223 <filter>output_options['out_add'] and "gz" in output_options['out_add']</filter>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
224 </data>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
225 <data name="short_report_pdf" format="pdf" label="${tool.name} on ${on_string}: short report (pdf)" from_work_dir="outputdir/short_report.pdf">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
226 <filter>output_options['out_sr'] and "pdf" in output_options['out_sr']</filter>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
227 </data>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
228 <data name="short_report_tex" format="txt" label="${tool.name} on ${on_string}: short report (tex)" from_work_dir="outputdir/short_report.tex">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
229 <filter>output_options['out_sr'] and "tex" in output_options['out_sr']</filter>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
230 </data>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
231 <data name="short_report_tabular" format="tabular" label="${tool.name} on ${on_string}: short report (tabular)" from_work_dir="outputdir/short_report.tsv">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
232 <filter>output_options['out_sr'] and "tabular" in output_options['out_sr']</filter>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
233 </data>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
234 </outputs>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
235 <tests>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
236 <!-- Test 01: Minimum input txt output-->
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
237 <test expect_num_outputs="1">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
238 <param name="transcripts" value="transcriptome01.fasta"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
239 <section name="output_options">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
240 <param name="out_sr" value="tabular"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
241 </section>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
242 <output name="short_report_tabular" file="test_01_short_report.tab"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
243 </test>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
244 <!-- Test 02: Transcriptome reference,single read, txt output-->
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
245 <test expect_num_outputs="1">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
246 <param name="transcripts" value="transcriptome01.fasta"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
247 <section name="output_options">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
248 <param name="out_sr" value="tabular"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
249 </section>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
250 <conditional name="reads_option">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
251 <param name="selector" value="single"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
252 <param name="single_reads" value="single_end.fastq.gz"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
253 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
254 <output name="short_report_tabular">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
255 <assert_contents>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
256 <has_text text="Transcripts" />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
257 <has_size value="95" delta="5"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
258 </assert_contents>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
259 </output>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
260 </test>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
261 <!-- Test 03: Transcriptome reference and annotation, txt output-->
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
262 <test expect_num_outputs="1">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
263 <param name="transcripts" value="transcriptome01.fasta"/>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
264 <conditional name="gene_coordinates">
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
265 <param name="selector" value="true"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
266 <param name="gtf" value="reference.gtf"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
267 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
268 <section name="output_options">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
269 <param name="out_sr" value="tabular"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
270 </section>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
271 <conditional name="reads_option">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
272 <param name="selector" value="single"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
273 <param name="single_reads" value=""/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
274 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
275 <output name="short_report_tabular" file="test_03_short_report.tab"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
276 </test>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
277 <!-- Test 04: Transcriptome reference and annotation, txt output-->
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
278 <test expect_num_outputs="1">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
279 <param name="transcripts" value="transcriptome01.fasta"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
280 <conditional name="gene_coordinates">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
281 <param name="selector" value="true"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
282 <param name="gtf" value="reference.gtf"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
283 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
284 <section name="output_options">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
285 <param name="out_sr" value="tabular"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
286 </section>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
287 <conditional name="reads_option">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
288 <param name="selector" value="single"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
289 <param name="single_reads" value="single_end.fastq.gz"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
290 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
291 <output name="short_report_tabular">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
292 <assert_contents>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
293 <has_text text="Transcripts" />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
294 <has_size value="140" delta="5"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
295 </assert_contents>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
296 </output>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
297 </test>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
298 <!-- Test 05: Transcriptome reference, annotation and mapping, txt output-->
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
299 <test expect_num_outputs="1">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
300 <param name="transcripts" value="transcriptome01.fasta"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
301 <conditional name="gene_coordinates">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
302 <param name="selector" value="true"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
303 <param name="gtf" value="reference.gtf"/>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
304 </conditional>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
305 <section name="output_options">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
306 <param name="out_sr" value="tabular"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
307 </section>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
308 <conditional name="reads_option">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
309 <param name="selector" value='paired'/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
310 <param name="forward_reads" value="input_F.fastqsanger"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
311 <param name="reverse_reads" value="input_F.fastqsanger"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
312 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
313 <output name="short_report_tabular">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
314 <assert_contents>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
315 <has_text text="Transcripts" />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
316 <has_size value="140" delta="5"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
317 </assert_contents>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
318 </output>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
319 </test>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
320 <!-- Test 06: Transcriptome reference, annotation, mapping and BUSCO, txt output-->
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
321 <test expect_num_outputs="1">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
322 <param name="transcripts" value="transcriptome01.fasta"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
323 <conditional name="gene_coordinates">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
324 <param name="selector" value="true"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
325 <param name="gtf" value="reference.gtf"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
326 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
327 <conditional name="reads_option">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
328 <param name="selector" value='paired'/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
329 <param name="forward_reads" value="input_F.fastqsanger"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
330 <param name="reverse_reads" value="input_R.fastqsanger"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
331 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
332 <section name="output_options">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
333 <param name="out_sr" value="tabular"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
334 </section>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
335 <conditional name="use_busco">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
336 <param name="selector" value="true"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
337 <conditional name="lineage_conditional">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
338 <param name="selector" value="cached"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
339 <param name="cached_db" value="busco-demo-db-20230328"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
340 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
341 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
342 <output name="short_report_tabular">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
343 <assert_contents>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
344 <has_text text="Transcripts" />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
345 <has_size value="140" delta="5"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
346 </assert_contents>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
347 </output>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
348 </test>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
349 <!-- Test 07: Transcriptome reference, annotation, mapping and BUSCO, additional outputs-->
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
350 <test expect_num_outputs="4">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
351 <param name="transcripts" value="transcriptome01.fasta"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
352 <conditional name="gene_coordinates">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
353 <param name="selector" value="true"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
354 <param name="gtf" value="reference.gtf"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
355 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
356 <param name="reference" value="reference.fasta"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
357 <conditional name="reads_option">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
358 <param name="selector" value='paired'/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
359 <param name="forward_reads" value="input_F.fastqsanger"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
360 <param name="reverse_reads" value="input_R.fastqsanger"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
361 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
362 <conditional name="use_busco">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
363 <param name="selector" value="true"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
364 <conditional name="lineage_conditional">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
365 <param name="selector" value="cached"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
366 <param name="cached_db" value="busco-demo-db-20230328"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
367 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
368 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
369 <section name="output_options">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
370 <param name="out_sr" value="pdf,tabular"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
371 <param name="out_add" value="fasta,gz"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
372 </section>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
373 <output_collection name="fasta_files" type="list" count="7">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
374 <element name="transcriptome01.paralogs" file="test_07_paralogs.fasta" ftype="fasta"/>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
375 </output_collection>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
376 <output name="short_report_pdf" file="test_07_short_report.pdf" ftype="pdf" compare="sim_size" delta="1000"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
377 <output name="short_report_tabular" file="test_07_short_report.tab" ftype="tabular"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
378 <output name="compressed_files" ftype="tgz">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
379 <assert_contents>
6
8e66f695d859 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 7536270b3b51024e516b840728db6e6d0f903f69
iuc
parents: 5
diff changeset
380 <has_archive_member path="./outputdir/.*" n="62" delta="0"/>
8e66f695d859 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 7536270b3b51024e516b840728db6e6d0f903f69
iuc
parents: 5
diff changeset
381 <has_archive_member path="./outputdir/logs/.*" n="10" delta="0"/>
8e66f695d859 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 7536270b3b51024e516b840728db6e6d0f903f69
iuc
parents: 5
diff changeset
382 <has_archive_member path="./outputdir/transcriptome01_output/.*" n="45" delta="0"/>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
383 </assert_contents>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
384 </output>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
385 </test>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
386 <!-- Test 08: Multiple inputs-->
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
387 <test expect_num_outputs="6">
7
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
388 <param name="transcripts" value="transcriptome01.fasta,transcriptome?02.fasta"/>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
389 <param name="reference" value="reference.fasta"/>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
390 <conditional name="gene_coordinates">
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
391 <param name="selector" value="true"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
392 <param name="gtf" value="reference.gtf"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
393 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
394 <section name="output_options">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
395 <param name="out_sr" value="tabular,pdf"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
396 </section>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
397 <conditional name="use_busco">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
398 <param name="selector" value="true"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
399 <conditional name="lineage_conditional">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
400 <param name="selector" value="cached"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
401 <param name="cached_db" value="busco-demo-db-20230328"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
402 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
403 </conditional>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
404 <param name="out_add" value="complete,fasta,logs,gz"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
405 <conditional name="reads_option">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
406 <param name="selector" value="single"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
407 <param name="single_reads" value="single_end.fastq.gz"/>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
408 </conditional>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
409 <output name="short_report_tabular" value="test_08_short_report.tab" ftype="tabular"/>
7
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
410 <output name="short_report_pdf" value="test_08_short_report.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
411 <output name="stats" value="test_08_complete_report.tab" ftype="txt" lines_diff="6" />
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
412 <output_collection name="fasta_files" type="list" count="14">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
413 <element name="transcriptome01.paralogs" file="test_08_paralogs.fasta" ftype="fasta"/>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
414 </output_collection>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
415 <output_collection name="list_logs" type="list" count="14">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
416 <element name="STAR.out" ftype="txt">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
417 <assert_contents>
8
f73ab5187eed planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 140ef122cde10b77c9c9466cf8464c1bce6599e9
iuc
parents: 7
diff changeset
418 <has_text_matching expression="STAR.* --runThreadN"/>
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
419 <has_text text="finished successfully"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
420 </assert_contents>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
421 </element>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
422 <element name="gmap_build.out" ftype="txt">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
423 <assert_contents>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
424 <has_text text="No alternate scaffolds observed"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
425 </assert_contents>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
426 </element>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
427 <element name="rnaQUAST" ftype="txt">
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
428 <assert_contents>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
429 <has_text text="THE QUALITY OF TRANSCRIPTOME ASSEMBLY DONE"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
430 <has_text text="Thank you for using rnaQUAST!"/>
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
431 </assert_contents>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
432 </element>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
433 </output_collection>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
434 </test>
7
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
435 <!-- Test 09: Multiple inputs with dash in names-->
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
436 <test expect_num_outputs="6">
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
437 <param name="transcripts" value="transcriptome01.fasta,transcriptome-02.fasta"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
438 <param name="reference" value="reference.fasta"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
439 <conditional name="gene_coordinates">
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
440 <param name="selector" value="true"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
441 <param name="gtf" value="reference.gtf"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
442 </conditional>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
443 <section name="output_options">
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
444 <param name="out_sr" value="tabular,pdf"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
445 </section>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
446 <conditional name="use_busco">
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
447 <param name="selector" value="true"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
448 <conditional name="lineage_conditional">
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
449 <param name="selector" value="cached"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
450 <param name="cached_db" value="busco-demo-db-20230328"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
451 </conditional>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
452 </conditional>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
453 <param name="out_add" value="complete,fasta,logs,gz"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
454 <conditional name="reads_option">
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
455 <param name="selector" value="single"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
456 <param name="single_reads" value="single_end.fastq.gz"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
457 </conditional>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
458 <output name="short_report_tabular" value="test_08_short_report.tab" ftype="tabular"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
459 <output name="short_report_pdf" value="test_08_short_report.pdf" ftype="pdf" compare="sim_size" delta_frac="0.1"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
460 <output name="stats" value="test_08_complete_report.tab" ftype="txt" lines_diff="6" />
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
461 <output_collection name="fasta_files" type="list" count="14">
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
462 <element name="transcriptome01.paralogs" file="test_08_paralogs.fasta" ftype="fasta"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
463 </output_collection>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
464 <output_collection name="list_logs" type="list" count="14">
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
465 <element name="STAR.out" ftype="txt">
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
466 <assert_contents>
8
f73ab5187eed planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 140ef122cde10b77c9c9466cf8464c1bce6599e9
iuc
parents: 7
diff changeset
467 <has_text_matching expression="STAR.* --runThreadN"/>
7
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
468 <has_text text="finished successfully"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
469 </assert_contents>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
470 </element>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
471 <element name="gmap_build.out" ftype="txt">
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
472 <assert_contents>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
473 <has_text text="No alternate scaffolds observed"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
474 </assert_contents>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
475 </element>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
476 <element name="rnaQUAST" ftype="txt">
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
477 <assert_contents>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
478 <has_text text="THE QUALITY OF TRANSCRIPTOME ASSEMBLY DONE"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
479 <has_text text="Thank you for using rnaQUAST!"/>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
480 </assert_contents>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
481 </element>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
482 </output_collection>
3125faf00ffd planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit d68ebc953fe79f2909c79ef1b133300f450aa822
iuc
parents: 6
diff changeset
483 </test>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
484 </tests>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
485 <help><![CDATA[
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
486
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
487 .. class:: infomark
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
488
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
489 **Purpose**
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
490
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
491 rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
492 of estimating gene database coverage by raw reads and de novo quality assessment.
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
493
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
494 .. class:: infomark
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
495
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
496 **rnaQUAST pipeline**
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
497
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
498 To evaluate quality of the assembled transcripts, rnaQUAST takes a reference genome in FASTA format and optionally its gene database in
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
499 GFF/GTF format. A user can provide either a FASTA file with transcripts, which will be aligned to the given reference genome using GMAP
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
500 or BLAT. The alignments are analyzed to calculate simple metrics and then are matched against the isoforms from the gene database in order
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
501 to obtain statistics that represent completeness and correctness levels of the assembly. In addition, rnaQUAST is capable of estimating
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
502 gene database coverage by raw reads using STAR or TopHat2. For de novo quality assessment when reference genome and gene database are
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
503 unavailable, the transcripts are analyzed using BUSCO.
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
504
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
505 .. class:: infomark
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
506
5
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
507 **Metrics and alignment analysis**
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
508
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
509 rnaQUAST calculates various metrics without using alignment information, e.g. length distribution and N50 of the assembled transcripts.
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
510 Additionally, rnaQUAST computes the following statistics for the gene database: the total number of genes and isoforms, isoform and exon
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
511 length distribution, average number of exons per gene, etc.
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
512
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
513 To analyze transcripts' alignments, rnaQUAST firstly filters out short partial alignments (shorter than a user-defined threshold, default
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
514 value is 50 bp). Such short alignments are typically caused by genomic repeats and thus are ignored. Afterwards, rnaQUAST selects the
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
515 best-scored spliced alignment for each transcript. If a transcript has more than one alignment with the highest score, it is reported
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
516 as multiply aligned. Otherwise, it is considered to be uniquely aligned. If the best-scored alignment is discordant (e.g. the transcript
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
517 has partial alignments that are either mapped to different strands or to different chromosomes) the transcript is classified as misassembled.
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
518 Transcripts without misassemblies are analyzed to calculate such metrics as average transcript alignment fraction and mismatch rate.
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
519
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
520 For the simplicity of explanation, transcript is further referred to as a sequence generated by the assembler and isoform denotes a sequence
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
521 from the gene database. rnaQUAST matches best-scored alignments of non-misassembled transcripts to the isoforms' coordinates and analyzes
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
522 them to estimate how well the isoforms are covered by the assembly. rnaQUAST computes such metrics as database coverage (the total number
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
523 of covered bases of all isoforms divided by the total length of all isoforms) and the number of 50%/95%-assembled isoforms. An isoform is
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
524 considered to be x%-assembled if it has at least x% covered by a single transcript. Vice versa, to evaluate how well the assembled
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
525 transcripts are covered by the isoforms, rnaQUAST estimates the number of unannotated transcripts (that align to the genome, but do not
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
526 match to any isoform) and the number of 50%/95%-matched transcripts (that have corresponding fraction mapped to an isoform). Indeed, the
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
527 thresholds described above (50% and 95%) can be varied by the user.
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
528
f89e3c318453 planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit c633f5c634128e3c81ab48e94df6f703dd005c46
iuc
parents: 4
diff changeset
529
1
e989670c7fc7 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit dc0a0cf275168c2a88ee3dc47652dd7ca1137871"
iuc
parents: 0
diff changeset
530 ]]> </help>
0
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
531 <citations>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
532 <citation type="doi">10.1093/bioinformatics/btw218 </citation>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
533 </citations>
33c060ec0ac9 "planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3"
iuc
parents:
diff changeset
534 </tool>