Mercurial > repos > iuc > samtools_fastx

annotate samtools_fastx.xml @ 5:344c3c1177a9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:22:32 +0000
parents 1c46e3315853
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
1 <tool id="samtools_fastx" name="Samtools fastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
2 <description>extract FASTA or FASTQ from alignment files</description>
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
3 <macros>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
4 <import>macros.xml</import>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
5 </macros>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
6 <expand macro="requirements" />
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
7 <expand macro="stdio"/>
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
8 <expand macro="version_command" />
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
9 <command><![CDATA[
3
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
10 @ADDTHREADS@
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
11 ## name sort input file if neccessary
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
12 #if not $input.is_of_type('qname_sorted.bam', 'qname_input_sorted.bam'):
2
af994f4458bc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
iuc
parents: 1
diff changeset
13 samtools sort -@ \$addthreads -n '$input' -T "\${TMPDIR:-.}" > input &&
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
14 #else:
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
15 ln -s '$input' input &&
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
16 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
17
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
18 #set command=str($output_fmt_cond.output_fmt_select)[:5]
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
19
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
20 samtools $command
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
21 #if str($output_fmt_cond.output_fmt_select).startswith('fastq'):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
22 #if str($output_fmt_cond.default_quality) != '':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
23 -v $output_fmt_cond.default_quality
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
24 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
25 $output_fmt_cond.output_quality
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
26 $output_fmt_cond.ilumina_casava
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
27 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
28 $copy_tags
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
29 #if str($copy_arb_tags) != '':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
30 -T '$copy_arb_tags'
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
31 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
32 $read_numbering
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
33 #if 'r0' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
34 -0 nonspecific.$output_fmt_cond.output_fmt_select
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
35 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
36 #if 'r1' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
37 -1 forward.$output_fmt_cond.output_fmt_select
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
38 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
39 #if 'r2' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
40 -2 reverse.$output_fmt_cond.output_fmt_select
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
41 #end if
3
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
42 #set $filter = $inclusive_filter
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
43 @FLAGS@
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
44 -f $flags
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
45 #set $filter = $exclusive_filter
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
46 @FLAGS@
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
47 -F $flags
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
48 #set $filter = $exclusive_filter_all
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
49 @FLAGS@
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
50 -G $flags
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
51 #if 's' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
52 -s singletons.$output_fmt_cond.output_fmt_select
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
53 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
54 #if str($idxout_cond.idxout_select) == 'yes':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
55 #if str($idxout_cond.write1st) == 'yes':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
56 --i1 i1.$output_fmt_cond.output_fmt_select
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
57 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
58 #if str($idxout_cond.write2nd) == 'yes':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
59 --i2 i2.$output_fmt_cond.output_fmt_select
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
60 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
61 #if str($idxout_cond.index_format) != '':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
62 --index-format $idxout_cond.index_format
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
63 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
64 #if str($idxout_cond.barcode_tag) != '':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
65 --barcode-tag $idxout_cond.barcode_tag
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
66 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
67 #if str($idxout_cond.quality_tag) != '':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
68 --quality-tag $idxout_cond.quality_tag
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
69 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
70 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
71
3
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
72 input
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
73
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
74 #if str($outputs)=='None' or 'other' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
75 ## since currently stdout in not zipped (samtools doesn't know about the extension)
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
76 #if str($output_fmt_cond.output_fmt_select).endswith('.gz'):
3
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
77 | gzip -
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
78 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
79 > output.$output_fmt_cond.output_fmt_select
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
80 && ln -s output.$output_fmt_cond.output_fmt_select output
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
81 #else
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
82 ## otherwise the remaining sequences would show up in the datasets info box
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
83 > /dev/null
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
84 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
85 #if 'r0' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
86 && ln -s nonspecific.$output_fmt_cond.output_fmt_select nonspecific
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
87 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
88 #if 'r1' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
89 && ln -s forward.$output_fmt_cond.output_fmt_select forward
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
90 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
91 #if 'r2' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
92 && ln -s reverse.$output_fmt_cond.output_fmt_select reverse
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
93 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
94 #if 's' in str($outputs):
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
95 && ln -s singletons.$output_fmt_cond.output_fmt_select singletons
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
96 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
97 #if str($idxout_cond.idxout_select) == 'yes':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
98 #if str($idxout_cond.write1st) == 'yes':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
99 && ln -s i1.$output_fmt_cond.output_fmt_select i1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
100 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
101 #if str($idxout_cond.write2nd) == 'yes':
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
102 && ln -s i2.$output_fmt_cond.output_fmt_select i2
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
103 #end if
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
104 #end if
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
105 ]]>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
106 </command>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
107 <inputs>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
108 <param name="input" type="data" format="sam,bam,cram" label="BAM or SAM file to convert" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
109 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
110 <param name="output_fmt_select" type="select" label="Output format">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
111 <option value="fasta" selected="True">FASTA</option>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
112 <option value="fastqsanger">FASTQ</option>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
113 <option value="fasta.gz">compressed FASTA</option>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
114 <option value="fastqsanger.gz">compressed FASTQ</option>
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
115 </param>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
116 <when value="fastqsanger">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
117 <param name="default_quality" argument="-v" type="integer" optional="True" label="Default quality if none is given" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
118 <param name="output_quality" argument="-O" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Output quality in the OQ tag if available" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
119 <param name="ilumina_casava" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)" />
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
120 </when>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
121 <when value="fasta" />
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
122 <when value="fastqsanger.gz">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
123 <param name="default_quality" argument="-v" type="integer" optional="True" label="Default quality if none is given" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
124 <param name="output_quality" argument="-O" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Output quality in the OQ tag if available" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
125 <param name="ilumina_casava" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
126 </when>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
127 <when value="fasta.gz" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
128 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
129 <param name="outputs" type="select" multiple="true" label="outputs">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
130 <option value="other" selected="true">others</option>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
131 <option value="r1">READ1</option>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
132 <option value="r2">READ2</option>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
133 <option value="s">singletons</option>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
134 <option value="r0">unspecific</option>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
135 <help>disjoint subsets of the reads can be redirected to separate data sets. "READ[12]" are reads for which the READ[12] flag is set and the READ[21] flag is not set. "unspecific" reads are those for which both ore neither of these flags are set. "singletons" are the singleto reads. Note that if selected READ1 and READ2 contain only the paired reads. "other" are the remaining reads. If onlz 'others' or nothing is selected all reads go to a single data set. </help>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
136 </param>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
137 <param name="copy_tags" argument="-t" type="boolean" truevalue="-t" falsevalue="" label="Copy RG/BC/QT tags to output header" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
138 <param name="copy_arb_tags" argument="-T" type="text" optional="true" label="copy arbitrary tags to the FASTA header line" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
139 <param name="read_numbering" type="select" label="Omit or append read numbers">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
140 <option value="" selected="True">no</option>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
141 <option value="-n">Do not append /1 and /2 to read names</option>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
142 <option value="-N">always append /1 and /2 to read name</option>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
143 </param>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
144 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set">
3
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
145 <expand macro="flag_options"/>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
146 </param>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
147 <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set">
3
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
148 <expand macro="flag_options" s256="true" s2048="true"/>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
149 </param>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
150 <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
151 <expand macro="flag_options" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
152 </param>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
153
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
154 <conditional name="idxout_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
155 <param name="idxout_select" type="select" label="Write index read files">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
156 <option value="no" selected="True">No</option>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
157 <option value="yes">Yes (beta: feedback welcome)</option>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
158 </param>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
159 <when value="no" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
160 <when value="yes">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
161 <param name="write1st" argument="--i1" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="write first index reads to extra data set" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
162 <param name="write2nd" argument="--i2" type="boolean" truevalue="yes" falsevalue="no" checked='true' label="write second index reads to extra data set" />
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
163 <param argument="--index-format" type="text" label="Index format: How to parse barcode and quality tags">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
164 <help>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
165 The index-format string describes how to parse the barcode and quality tags, for example:
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
166 i14i8 the first 14 characters are index 1, the next 8 characters are index 2
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
167 n8i14 ignore the first 8 characters, and use the next 14 characters for index 1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
168 If the tag contains a separator, then the numeric part can be replaced with '*' to mean
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
169 'read until the separator or end of tag', for example:
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
170 n*i* ignore the left part of the tag until the separator, then use the second part
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
171 of the tag as index 1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
172 </help>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
173 </param>
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
174 <param argument="--barcode-tag" type="text" optional="True" label="Barcode tag [default: BC]"/>
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
175 <param argument="--quality-tag" type="text" optional="True" label="Quality tag [default: QT]"/>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
176 </when>
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
177 </conditional>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
178 </inputs>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
179 <outputs>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
180 <data name="nonspecific" format="fasta" from_work_dir="nonspecific" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (nonspecific)">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
181 <filter>'r0' in str(outputs)</filter>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
182 <actions>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
183 <action type="format">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
184 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
185 </action>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
186 </actions>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
187 </data>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
188 <data name="forward" format="fasta" from_work_dir="forward" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (READ1)">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
189 <filter>'r1' in str(outputs)</filter>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
190 <actions>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
191 <action type="format">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
192 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
193 </action>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
194 </actions>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
195 </data>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
196 <data name="reverse" format="fasta" from_work_dir="reverse" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (READ2)">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
197 <filter>'r2' in str(outputs)</filter>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
198 <actions>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
199 <action type="format">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
200 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
201 </action>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
202 </actions>
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
203 </data>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
204 <data name="singletons" format="fasta" from_work_dir="singletons" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (singletons)">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
205 <filter>'s' in str(outputs)</filter>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
206 <actions>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
207 <action type="format">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
208 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
209 </action>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
210 </actions>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
211 </data>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
212 <data name="output" format="fasta" from_work_dir="output" label="${on_string} converted to ${output_fmt_cond.output_fmt_select}">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
213 <filter>str(outputs)=='None' or 'other' in str(outputs)</filter>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
214 <actions>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
215 <action type="format">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
216 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
217 </action>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
218 </actions>
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
219 </data>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
220 <data name="i1" format="fasta" from_work_dir="i1" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (1st index)">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
221 <filter>idxout_cond['idxout_select']=='yes' and idxout_cond['write1st']</filter>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
222 <actions>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
223 <action type="format">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
224 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
225 </action>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
226 </actions>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
227 </data>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
228 <data name="i2" format="fasta" from_work_dir="i2" label="${on_string} converted to ${output_fmt_cond.output_fmt_select} (2nd index)">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
229 <filter>idxout_cond['idxout_select']=='yes' and idxout_cond['write2nd']</filter>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
230 <actions>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
231 <action type="format">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
232 <option type="from_param" name="output_fmt_cond" param_attribute="output_fmt_select" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
233 </action>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
234 </actions>
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
235 </data>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
236 </outputs>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
237 <tests>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
238 <!-- tests from original Galaxy tool -->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
239 <test expect_num_outputs="1">
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
240 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
241 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
242 <param name="output_fmt_select" value="fasta" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
243 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
244 <param name="outputs" value="other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
245 <output name="output" file="samtools_fastx-out1.fasta" ftype="fasta" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
246 </test>
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
247 <test expect_num_outputs="3">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
248 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
249 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
250 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
251 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
252 <param name="outputs" value="r0,r1,r2" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
253 <output name="nonspecific" file="samtools_fastx-out2-1.fastq" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
254 <output name="forward" file="samtools_fastx-out2-2.fastq" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
255 <output name="reverse" file="samtools_fastx-out2-3.fastq" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
256 </test>
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
257 <test expect_num_outputs="3">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
258 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
259 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
260 <param name="output_fmt_select" value="fasta" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
261 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
262 <param name="outputs" value="r0,r1,r2" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
263 <output name="nonspecific" file="samtools_fastx-out3-1.fasta" ftype="fasta" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
264 <output name="forward" file="samtools_fastx-out3-2.fasta" ftype="fasta" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
265 <output name="reverse" file="samtools_fastx-out3-3.fasta" ftype="fasta" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
266 </test>
3
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
267 <!-- tests from original Galaxy tool with gz output. for some reason gzip (which is used
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
268 for compressing stdout does not give exactly the same file contents .. the other
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
269 compressed files seem to)-->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
270 <test expect_num_outputs="1">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
271 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
272 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
273 <param name="output_fmt_select" value="fasta.gz" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
274 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
275 <param name="outputs" value="other" />
3
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
276 <output name="output" file="samtools_fastx-out1.fasta.gz" ftype="fasta.gz" decompress="true"/>
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
277 </test>
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
278 <test expect_num_outputs="3">
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
279 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
280 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
281 <param name="output_fmt_select" value="fastqsanger.gz" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
282 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
283 <param name="outputs" value="r0,r1,r2" />
3
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
284 <output name="nonspecific" file="samtools_fastx-out2-1.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
285 <output name="forward" file="samtools_fastx-out2-2.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
286 <output name="reverse" file="samtools_fastx-out2-3.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
287 </test>
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
288 <test expect_num_outputs="3">
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
289 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
290 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
291 <param name="output_fmt_select" value="fasta.gz" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
292 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
293 <param name="outputs" value="r0,r1,r2" />
3
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
294 <output name="nonspecific" file="samtools_fastx-out3-1.fasta.gz" ftype="fasta.gz" decompress="true" />
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
295 <output name="forward" file="samtools_fastx-out3-2.fasta.gz" ftype="fasta.gz" decompress="true" />
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
296 <output name="reverse" file="samtools_fastx-out3-3.fasta.gz" ftype="fasta.gz" decompress="true" />
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
297 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
298 <!-- tests from: https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2313-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
299 <!--# basic 2 output test without singleton tracking-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
300 <!--test_cmd($opts, out=>'bam2fq/1.stdout.expected', out_map=>{'1.fq' => 'bam2fq/1.1.fq.expected', '2.fq' => 'bam2fq/1.2.fq.expected'},cmd=>"$$opts{bin}/samtools fastq @$threads -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");-->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
301 <test expect_num_outputs="3">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
302 <param name="input" value="bam2fq.001.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
303 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
304 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
305 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
306 <param name="outputs" value="r1,r2,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
307 <output name="forward" file="1.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
308 <output name="reverse" file="1.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
309 <output name="output" file="1.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
310 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
311 <!--# basic 2 output test with singleton tracking but no singleton-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
312 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/2.1.fq.expected', '2.fq' => 'bam2fq/2.2.fq.expected', 's.fq' => 'bam2fq/2.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.001.sam");-->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
313 <test expect_num_outputs="4">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
314 <param name="input" value="bam2fq.001.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
315 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
316 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
317 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
318 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
319 <output name="forward" file="2.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
320 <output name="reverse" file="2.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
321 <output name="singletons" file="2.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
322 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
323 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
324 <!--# basic 2 output test with singleton tracking with a singleton in the middle-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
325 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/3.1.fq.expected', '2.fq' => 'bam2fq/3.2.fq.expected', 's.fq' => 'bam2fq/3.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.002.sam");-->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
326 <test expect_num_outputs="4">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
327 <param name="input" value="bam2fq.002.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
328 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
329 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
330 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
331 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
332 <output name="forward" file="3.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
333 <output name="reverse" file="3.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
334 <output name="singletons" file="3.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
335 <output name="output" file="3.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
336 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
337 <!--# basic 2 output test with singleton tracking with a singleton as last read-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
338 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.003.sam");-->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
339 <test expect_num_outputs="4">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
340 <param name="input" value="bam2fq.003.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
341 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
342 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
343 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
344 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
345 <output name="forward" file="4.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
346 <output name="reverse" file="4.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
347 <output name="singletons" file="4.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
348 <output name="output" file="4.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
349 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
350 <!--# tag output test with singleton tracking with a singleton as last read-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
351 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
352 <test expect_num_outputs="5">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
353 <param name="input" value="bam2fq.004.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
354 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
355 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
356 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
357 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
358 <conditional name="idxout_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
359 <param name="idxout_select" value="yes"/>
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
360 <param name="write1st" value="true"/>
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
361 <param name="write2nd" value="false"/>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
362 <param name="barcode_tag" value="BC"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
363 <param name="index_format" value="n2i2"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
364 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
365 <output name="forward" file="4.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
366 <output name="reverse" file="4.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
367 <output name="singletons" file="4.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
368 <output name="output" file="4.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
369 <output name="i1" file="bc.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
370 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
371 <!--# test -O flag with no OQ tags-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
372 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/4.1.fq.expected', '2.fq' => 'bam2fq/4.2.fq.expected', 's.fq' => 'bam2fq/4.s.fq.expected', 'bc.fq' => 'bam2fq/bc.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
373 <test expect_num_outputs="5">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
374 <param name="input" value="bam2fq.010.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
375 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
376 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
377 <param name="output_quality" value="-O" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
378 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
379 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
380 <conditional name="idxout_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
381 <param name="idxout_select" value="yes"/>
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
382 <param name="write1st" value="true"/>
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
383 <param name="write2nd" value="false"/>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
384 <param name="barcode_tag" value="BC"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
385 <param name="index_format" value="n2i2"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
386 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
387 <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
388 <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
389 <output name="singletons" file="10.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
390 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
391 <output name="i1" file="bc10.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
392 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
393 <!--# test -O flag with OQ tags-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
394 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/10.1.fq.expected', '2.fq' => 'bam2fq/10.2.fq.expected', 's.fq' => 'bam2fq/10.s.fq.expected', 'bc.fq' => 'bam2fq/bc10.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -O \-\-index-format 'n2i2' \-\-i1 $$opts{path}/bc.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.010.sam");-->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
395 <test expect_num_outputs="5">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
396 <param name="input" value="bam2fq.010.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
397 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
398 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
399 <param name="output_quality" value="-O" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
400 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
401 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
402 <conditional name="idxout_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
403 <param name="idxout_select" value="yes"/>
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
404 <param name="write1st" value="true"/>
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
405 <param name="write2nd" value="false"/>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
406 <param name="barcode_tag" value="BC"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
407 <param name="index_format" value="n2i2"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
408 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
409 <output name="forward" file="10.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
410 <output name="reverse" file="10.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
411 <output name="singletons" file="10.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
412 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
413 <output name="i1" file="bc10.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
414 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
415 <!--# tag output test with separators and -N flag-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
416 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/5.1.fq.expected', '2.fq' => 'bam2fq/5.2.fq.expected', 's.fq' => 'bam2fq/5.s.fq.expected', 'bc_split.fq' => 'bam2fq/bc_split.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -N \-\-index-format 'n*i*' \-\-i1 $$opts{path}/bc_split.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
417 <test expect_num_outputs="5">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
418 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
419 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
420 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
421 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
422 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
423 <param name="read_numbering" value="-N"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
424 <conditional name="idxout_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
425 <param name="idxout_select" value="yes"/>
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
426 <param name="write1st" value="true"/>
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
427 <param name="write2nd" value="false"/>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
428 <param name="barcode_tag" value="BC"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
429 <param name="index_format" value="n*i*"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
430 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
431 <output name="forward" file="5.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
432 <output name="reverse" file="5.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
433 <output name="singletons" file="5.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
434 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
435 <output name="i1" file="bc_split.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
436 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
437 <!--# -t flag-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
438 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/6.1.fq.expected', '2.fq' => 'bam2fq/6.2.fq.expected', 's.fq' => 'bam2fq/6.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
439 <test expect_num_outputs="4">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
440 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
441 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
442 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
443 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
444 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
445 <param name="copy_tags" value="-t" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
446 <param name="read_numbering" value="-N"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
447 <output name="forward" file="6.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
448 <output name="reverse" file="6.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
449 <output name="singletons" file="6.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
450 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
451 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
452 <!--# -T flag-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
453 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
454 <test expect_num_outputs="4">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
455 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
456 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
457 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
458 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
459 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
460 <param name="copy_tags" value="-t" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
461 <param name="copy_arb_tags" value="MD,ia" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
462 <param name="read_numbering" value="-N"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
463 <output name="forward" file="7.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
464 <output name="reverse" file="7.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
465 <output name="singletons" file="7.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
466 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
467 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
468 <!--# -i flag with no index-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
469 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/7.1.fq.expected', '2.fq' => 'bam2fq/7.2.fq.expected', 's.fq' => 'bam2fq/7.s.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads -N -t -i -T MD,ia -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.005.sam");-->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
470 <test expect_num_outputs="6">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
471 <param name="input" value="bam2fq.005.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
472 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
473 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
474 <param name="ilumina_casava" value="-i" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
475 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
476 <param name="outputs" value="r1,r2,s,other" />
3
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
477 <conditional name="idxout_cond">
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
478 <param name="idxout_select" value="yes"/>
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
479 <param name="index_format" value="n2i2"/>
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
480 </conditional>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
481 <param name="copy_tags" value="-t" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
482 <param name="copy_arb_tags" value="MD,ia" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
483 <param name="read_numbering" value="-N"/>
3
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
484 <output name="forward" file="11.1.fq.expected" ftype="fastqsanger" />
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
485 <output name="reverse" file="11.2.fq.expected" ftype="fastqsanger" />
c933a9166b1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents: 2
diff changeset
486 <output name="singletons" file="11.s.fq.expected" ftype="fastqsanger" />
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
487 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
488 <output name="i1" file="11.i.fq.expected" ftype="fastqsanger" />
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
489 <output name="i2" file="11.i2.fq.expected" ftype="fastqsanger" />
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
490 </test>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
491 <!--# -i flag with index-->
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
492 <!--test_cmd($opts, out=>'bam2fq/2.stdout.expected', out_map=>{'1.fq' => 'bam2fq/8.1.fq.expected', '2.fq' => 'bam2fq/8.2.fq.expected', 's.fq' => 'bam2fq/8.s.fq.expected', 'i.fq' => 'bam2fq/8.i.fq.expected'}, cmd=>"$$opts{bin}/samtools fastq @$threads \-\-barcode-tag BC -i \-\-index-format 'n2i2' \-\-i1 $$opts{path}/i.fq -s $$opts{path}/s.fq -1 $$opts{path}/1.fq -2 $$opts{path}/2.fq $$opts{path}/dat/bam2fq.004.sam");-->
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
493 <test expect_num_outputs="6">
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
494 <param name="input" value="bam2fq.004.sam" ftype="sam" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
495 <conditional name="output_fmt_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
496 <param name="output_fmt_select" value="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
497 <param name="ilumina_casava" value="-i" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
498 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
499 <param name="outputs" value="r1,r2,s,other" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
500 <conditional name="idxout_cond">
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
501 <param name="idxout_select" value="yes"/>
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
502 <param name="write1st" value="true"/>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
503 <param name="barcode_tag" value="BC"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
504 <param name="index_format" value="n2i2"/>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
505 </conditional>
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
506 <output name="forward" file="8.1.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
507 <output name="reverse" file="8.2.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
508 <output name="singletons" file="8.s.fq.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
509 <output name="output" file="2.stdout.expected" ftype="fastqsanger" />
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
510 <output name="i1" file="8.i.fq.expected" ftype="fastqsanger" />
5
344c3c1177a9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
iuc
parents: 4
diff changeset
511 <output name="i2" file="8.i2.fq.expected" ftype="fastqsanger" />
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
512 </test>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
513 </tests>
1
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
514 <help><![CDATA[
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
515 This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
516 SAM or BAM file in FASTA or FASTQ format.
a5429e2e18e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 60257e09a1aadf54bb2f06cbe1e88db6fd835e83
iuc
parents: 0
diff changeset
517 ]]>
0
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
518 </help>
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
519 <expand macro="citations" />
8d4e157baaec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 767cbc1eb097c97a9a98b26571d3ded17b8c9755
iuc
parents:
diff changeset
520 </tool>