Mercurial > repos > iuc > hisat2
annotate hisat2_macros.xml @ 14:526b91fbde60 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
author | iuc |
---|---|
date | Wed, 19 Jul 2017 04:57:27 -0400 |
parents | f4fa77189eb0 |
children | d5fe9aead222 |
rev | line source |
---|---|
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
2 <macros> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
3 <xml name="single_paired_selector"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
4 <param name="paired_selector" type="select" label="Single end or paired reads?"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
5 <option value="paired">Paired reads</option> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
6 <option value="single">Unpaired reads</option> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
7 </param> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
8 </xml> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
9 <xml name="paired_input_conditional" tokens="ftype"> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
10 <conditional name="paired"> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
11 <expand macro="single_paired_selector" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
12 <when value="paired"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
13 <conditional name="collection" label="Data structure"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
14 <param name="collection_selector" type="select" label="Input is structured as" help="If a list of pairs is selected, HISAT2 will run in batch mode over each pair in the list, producing a list of output bam files"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
15 <option value="files">Individual files</option> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
16 <option value="collection">Pair collection or list of pairs</option> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
17 </param> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
18 <when value="collection"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
19 <param name="reads" type="data_collection" collection_type="paired" format="@FTYPE@" label="Paired reads" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
20 </when> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
21 <when value="files"> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
22 <param name="forward" type="data" format="@FTYPE@" label="Forward reads" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
23 <param name="reverse" type="data" format="@FTYPE@" label="Reverse reads" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
24 </when> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
25 </conditional> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
26 <expand macro="paired_end_conditional" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
2
diff
changeset
|
27 <expand macro="paired_end_output" /> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
28 </when> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
29 <when value="single"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
30 <param name="reads" type="data" format="@FTYPE@" label="Reads" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
31 <param name="unaligned_file" argument="--un-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
32 <param name="aligned_file" argument="--al-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" /> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
33 </when> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
34 </conditional> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
35 </xml> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
36 <xml name="paired_end_conditional"> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
37 <conditional name="paired_end_options"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
38 <param name="paired_end_options_selector" type="select" label="Paired-end options"> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
39 <option value="defaults">Use default values</option> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
40 <option value="advanced">Specify paired-end parameters</option> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
41 </param> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
42 <when value="defaults" /> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
43 <when value="advanced"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
44 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" label="Disable alignments of individual mates" help="By default, when hisat cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
45 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" label="Disable alignments of individual mates" help="By default, hisat looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
46 <param name="skip_reverse" type="boolean" truevalue="--norc" falsevalue="" label="Skip reference strand of reference" help="If --norc is specified, hisat will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand" /> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
47 </when> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
48 </conditional> |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
49 </xml> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
2
diff
changeset
|
50 <xml name="paired_end_output"> |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
51 <param name="unaligned_file" argument="--un-conc-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" /> |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
52 <param name="aligned_file" argument="--al-conc-gz" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" /> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
2
diff
changeset
|
53 </xml> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
54 <token name="@paired_end_options@"> |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
2
diff
changeset
|
55 #if str( $input_format.paired.unaligned_file ) == "true": |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
56 #if $compressed == "GZ": |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
57 --un-conc-gz '${output_unaligned_reads_l}' |
11
e926afbd9e10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 2d92a777711babd19c84dfa0db806d33e386afc7-dirty
iuc
parents:
10
diff
changeset
|
58 #else if $compressed == "BZ2": |
e926afbd9e10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 2d92a777711babd19c84dfa0db806d33e386afc7-dirty
iuc
parents:
10
diff
changeset
|
59 --un-conc-bz2 '${output_unaligned_reads_l}' |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
60 #else: |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
61 --un-conc '${output_unaligned_reads_l}' |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
62 #end if |
7
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
2
diff
changeset
|
63 #end if |
5ba8e317529a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde
iuc
parents:
2
diff
changeset
|
64 #if str( $input_format.paired.aligned_file ) == "true": |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
65 #if $compressed == "GZ": |
11
e926afbd9e10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 2d92a777711babd19c84dfa0db806d33e386afc7-dirty
iuc
parents:
10
diff
changeset
|
66 --al-conc-gz '${output_aligned_reads_l}' |
e926afbd9e10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 2d92a777711babd19c84dfa0db806d33e386afc7-dirty
iuc
parents:
10
diff
changeset
|
67 #else if $compressed == "BZ2" |
e926afbd9e10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 2d92a777711babd19c84dfa0db806d33e386afc7-dirty
iuc
parents:
10
diff
changeset
|
68 --al-conc-bz2 '${output_aligned_reads_l}' |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
69 #else: |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
70 --al-conc '${output_aligned_reads_l}' |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
71 #end if |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
72 #end if |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
73 #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced': |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
74 ${input_format.paired.paired_end_options.no_mixed} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
75 ${input_format.paired.paired_end_options.no_discordant} |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
76 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
77 </token> |
2
c37b4554f794
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit a2aaa7c9fe7b343f95450ec428250317696a9fb7
iuc
parents:
0
diff
changeset
|
78 <token name="@strandedness_parameters@"> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
79 #if str($spliced_options.spliced_options_selector) == "advanced": |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
80 #if str($spliced_options.rna_strandness).strip() != '': |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
81 --rna-strandness $spliced_options.rna_strandness |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
82 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
83 #end if |
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
84 </token> |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
85 <token name="@FASTQGZ_SETUP@"> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
86 <![CDATA[ |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
87 #set compressed="False" |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
88 #if str($input_format.paired.paired_selector) == 'paired': |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
89 #if str($input_format.paired.collection.collection_selector) == 'collection': |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
90 #if $input_format.paired.collection.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"): |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
91 #set read1 = "input_f.fastq.gz" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
92 #set compressed = "GZ" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
93 #else if $input_format.paired.collection.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
94 #set read1 = "input_f.fastq.bz2" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
95 #set compressed = "BZ2" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
96 #else: |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
97 #set read1 = "input_f.fastq" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
98 #end if |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
99 ln -f -s '${input_format.paired.collection.reads.forward}' ${read1} && |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
100 |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
101 #if $input_format.paired.collection.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
102 #set read2 = "input_r.fastq.gz" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
103 #set compressed = "GZ" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
104 #else if $input_format.paired.collection.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
105 #set read2 = "input_r.fastq.bz2" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
106 #set compressed = "BZ2" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
107 #else: |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
108 #set read2 = "input_r.fastq" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
109 #end if |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
110 ln -f -s '${input_format.paired.collection.reads.reverse}' ${read2} && |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
111 #else: |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
112 #if $input_format.paired.collection.forward.is_of_type("fastq.gz", "fastqsanger.gz"): |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
113 #set read1 = "input_f.fastq.gz" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
114 #set compressed = "GZ" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
115 #else if $input_format.paired.collection.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
116 #set read1 = "input_f.fastq.bz2" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
117 #set compressed = "BZ2" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
118 #else: |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
119 #set read1 = "input_f.fastq" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
120 #end if |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
121 ln -f -s '${input_format.paired.collection.forward}' ${read1} && |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
122 |
14
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
123 #if $input_format.paired.collection.reverse.is_of_type("fastq.gz", "fastqsanger.gz"): |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
124 #set read2 = "input_r.fastq.gz" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
125 #set compressed = "GZ" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
126 #else if $input_format.paired.collection.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
127 #set read2 = "input_r.fastq.bz2" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
128 #set compressed = "BZ2" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
129 #else: |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
130 #set read2 = "input_r.fastq" |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
131 #end if |
526b91fbde60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5d57e4f6fdaed9e042c334fbe76f3f41ceb4fbc2
iuc
parents:
13
diff
changeset
|
132 ln -f -s '${input_format.paired.collection.reverse}' ${read2} && |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
133 #end if |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
134 #else: |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
135 #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"): |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
136 #set read1 = "input_f.fastq.gz" |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
137 #set compressed = "GZ" |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
138 #else if $input_format.paired.reads.is_of_type("fastq.bz2", "fastqsanger.bz2"): |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
139 #set read1 = "input_f.fastq.bz2" |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
140 #set compressed = "BZ2" |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
141 #else: |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
142 #set read1 = "input_f.fastq" |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
143 #end if |
11
e926afbd9e10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 2d92a777711babd19c84dfa0db806d33e386afc7-dirty
iuc
parents:
10
diff
changeset
|
144 ln -s '${input_format.paired.reads}' ${read1} && |
10
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
145 #end if |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
146 ]]> |
da8d655e2154
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890
iuc
parents:
7
diff
changeset
|
147 </token> |
0
5bafe7d7a55e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
148 </macros> |