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comparison trinity.xml @ 28:7f916fe93c16 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
author iuc
date Wed, 12 May 2021 08:41:44 +0000
parents 20fb86e85c0f
children e8aca4d11bc0
comparison
equal deleted inserted replaced
27:20fb86e85c0f 28:7f916fe93c16
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"/>