Mercurial > repos > iuc > trinity
comparison trinity.xml @ 27:5b60313a6ce7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
author | iuc |
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date | Wed, 12 May 2021 08:54:43 +0000 |
parents | 26d5493b20b6 |
children | 48636f857c4b |
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26:26d5493b20b6 | 27:5b60313a6ce7 |
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18 | 18 |
19 #if $additional_params.guided.is_guided == "yes": | 19 #if $additional_params.guided.is_guided == "yes": |
20 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' && | 20 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' && |
21 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' && | 21 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' && |
22 #end if | 22 #end if |
23 #if $pool.pool_mode == "Yes": | |
24 #if str($pool.inputs.paired_or_single) == "single": | |
25 #for i, f in enumerate($pool.inputs.input): | |
26 ln -s '$f' input${i}.${f.ext} && | |
27 #end for | |
28 #elif str($pool.inputs.paired_or_single) == "paired": | |
29 #for i, f in enumerate($pool.inputs.left_input): | |
30 ln -s '$f' left_input${i}.${f.ext} && | |
31 #end for | |
32 #for i, f in enumerate($pool.inputs.right_input): | |
33 ln -s '$f' right_input${i}.${f.ext} && | |
34 #end for | |
35 #elif str($pool.inputs.paired_or_single) == "paired_collection": | |
36 #for i, f in enumerate($pool.inputs.pair_input): | |
37 ln -s '$f.forward' 'left_input${i}.${f.forward.ext}' && | |
38 ln -s '$f.reverse' 'right_input${i}.${f.reverse.ext}' && | |
39 #end for | |
40 #end if | |
41 #elif $pool.pool_mode == "No": | |
42 #if $pool.inputs.paired_or_single == "unmerged_paired_collection": | |
43 ln -s '$pool.inputs.pair_input.forward' 'left_input.${$pool.inputs.pair_input.forward.ext}' && | |
44 ln -s '$pool.inputs.pair_input.reverse' 'right_input.${pool.inputs.pair_input.reverse.ext}' && | |
45 #elif $pool.inputs.paired_or_single == "unmerged_single_collection": | |
46 ln -s '$pool.inputs.input' 'input.${pool.inputs.input.ext}' && | |
47 #end if | |
48 #end if | |
49 | |
23 Trinity --no_version_check | 50 Trinity --no_version_check |
24 | 51 |
25 ## Inputs | 52 ## Inputs |
26 #if $pool.pool_mode == "Yes": | 53 #if $pool.pool_mode == "Yes": |
27 #if str($pool.inputs.paired_or_single) == "single": | 54 #if str($pool.inputs.paired_or_single) == "single": |
28 --single ${ ','.join(['"%s"' % x for x in $pool.inputs.input]) } | 55 --single ${ ','.join(["'input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.input)]) } |
29 #if $pool.inputs.input[0].is_of_type('fasta'): | 56 #if $pool.inputs.input[0].is_of_type('fasta'): |
30 --seqType fa | 57 --seqType fa |
31 #else: | 58 #else: |
32 --seqType fq | 59 --seqType fq |
33 #end if | 60 #end if |
34 | 61 |
35 #if $pool.inputs.strand.is_strand_specific: | 62 #if $pool.inputs.strand.is_strand_specific: |
36 --SS_lib_type $pool.inputs.strand.library_type | 63 --SS_lib_type $pool.inputs.strand.library_type |
37 #end if | 64 #end if |
38 #elif str($pool.inputs.paired_or_single) == "paired": | 65 #elif str($pool.inputs.paired_or_single) == "paired": |
39 --left ${ ','.join(['"%s"' % x for x in $pool.inputs.left_input]) } | 66 --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.left_input)]) } |
40 | 67 |
41 --right ${ ','.join(['"%s"' % x for x in $pool.inputs.right_input]) } | 68 --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.right_input)]) } |
42 | 69 |
43 #if $pool.inputs.left_input[0].is_of_type('fasta'): | 70 #if $pool.inputs.left_input[0].is_of_type('fasta'): |
44 --seqType fa | 71 --seqType fa |
45 #else: | 72 #else: |
46 --seqType fq | 73 --seqType fq |
47 #end if | 74 #end if |
48 @COMMAND_PAIRED_STRAND_JACCARD@ | 75 @COMMAND_PAIRED_STRAND_JACCARD@ |
49 #elif str($pool.inputs.paired_or_single) == "paired_collection": | 76 #elif str($pool.inputs.paired_or_single) == "paired_collection": |
50 --left ${ ','.join(['"%s"' % x.forward for x in $pool.inputs.pair_input]) } | 77 --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.forward.ext) for i, f in enumerate($pool.inputs.pair_input)]) } |
51 --right ${ ','.join(['"%s"' % x.reverse for x in $pool.inputs.pair_input]) } | 78 --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.reverse.ext) for i, f in enumerate($pool.inputs.pair_input)]) } |
52 #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'): | 79 #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'): |
53 --seqType fa | 80 --seqType fa |
54 #else: | 81 #else: |
55 --seqType fq | 82 --seqType fq |
56 #end if | 83 #end if |
57 @COMMAND_PAIRED_STRAND_JACCARD@ | 84 @COMMAND_PAIRED_STRAND_JACCARD@ |
58 #end if | 85 #end if |
59 #elif $pool.pool_mode == "No": | 86 #elif $pool.pool_mode == "No": |
60 #if $pool.inputs.paired_or_single == "unmerged_paired_collection": | 87 #if $pool.inputs.paired_or_single == "unmerged_paired_collection": |
61 --left $pool.inputs.pair_input.forward | 88 --left 'left_input.${$pool.inputs.pair_input.forward.ext}' |
62 | 89 |
63 --right $pool.inputs.pair_input.reverse | 90 --right 'right_input.${pool.inputs.pair_input.reverse.ext}' |
64 | 91 |
65 #if $pool.inputs.pair_input.forward.is_of_type('fasta'): | 92 #if $pool.inputs.pair_input.forward.is_of_type('fasta'): |
66 --seqType fa | 93 --seqType fa |
67 #else: | 94 #else: |
68 --seqType fq | 95 --seqType fq |
69 #end if | 96 #end if |
70 @COMMAND_PAIRED_STRAND_JACCARD@ | 97 @COMMAND_PAIRED_STRAND_JACCARD@ |
71 #elif $pool.inputs.paired_or_single == "unmerged_single_collection": | 98 #elif $pool.inputs.paired_or_single == "unmerged_single_collection": |
72 --single $pool.inputs.input | 99 --single 'input.${pool.inputs.input.ext}' |
73 | 100 |
74 #if $pool.inputs.input.is_of_type('fasta'): | 101 #if $pool.inputs.input.is_of_type('fasta'): |
75 --seqType fa | 102 --seqType fa |
76 #else: | 103 #else: |
77 --seqType fq | 104 --seqType fq |
78 #end if | 105 #end if |
79 | 106 |
237 <test> | 264 <test> |
238 <param name="pool_mode" value="No" /> | 265 <param name="pool_mode" value="No" /> |
239 <param name="paired_or_single" value="unmerged_paired_collection"/> | 266 <param name="paired_or_single" value="unmerged_paired_collection"/> |
240 <param name="pair_input"> | 267 <param name="pair_input"> |
241 <collection type="paired"> | 268 <collection type="paired"> |
242 <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger" /> | 269 <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger.gz" /> |
243 <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger"/> | 270 <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger.gz" /> |
244 </collection> | 271 </collection> |
245 </param> | 272 </param> |
246 <param name="is_strand_specific" value="true"/> | 273 <param name="is_strand_specific" value="true"/> |
247 <param name="norm" value="true"/> | 274 <param name="norm" value="true"/> |
248 <param name="library_type" value="RF"/> | 275 <param name="library_type" value="RF"/> |