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comparison qiime2/qiime_tools_import.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
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13:887cd4ad8e16 14:a0a8d77a991c
17 #set $semantic_type = $type_temp 17 #set $semantic_type = $type_temp
18 #end if 18 #end if
19 19
20 #def is_fastq($f_test) 20 #def is_fastq($f_test)
21 #set $f = open($f_test, 'rb') 21 #set $f = open($f_test, 'rb')
22 #set $fastq = str($f.readline()[0])
22 #if str($f.readline()[0]) == '@' 23 #if str($f.readline()[0]) == '@'
23 #$f.close() 24 #$f.close()
24 #return True 25 #return True
25 #end if 26 #end if
26 27
27 #$f.close() 28 #$f.close()
28 #return False 29 #return $fastq
29 #end def 30 #end def
30 31
31 32
32 ## Symlinks creation or On the fly creation of a combo file 33 ## Symlinks creation or On the fly creation of a combo file
33 #if $input_type.type == 'list_list' 34 #if $input_type.type == 'list_list'
34 ## Symlinks creation or On the fly creation of a combo file 35 ## Symlinks creation or On the fly creation of a combo file
35 #for $f in $input_type.list_list: 36 #for $f in $input_type.list_list:
36 37
37 #set $is_fastq_file = $is_fastq(str($f)) 38 #set $is_fastq_file = $is_fastq(str($f))
38 39
39 #if $is_fastq_file: 40 #if $is_fastq_file:
40 #set $file_for_processing = "'input/" + $f.name + '.gz' + "'" 41 #set $file_for_processing = "'input/" + $f.name + '.gz' + "'"
41 gzip -c ${f} > $file_for_processing; 42 gzip -c ${f} > $file_for_processing;
43 ##echo $is_fastq_file;
42 #else 44 #else
43 #set $file_for_processing = "'input/" + $f.name + "'" 45 #set $file_for_processing = "'input/" + $f.name + "'"
44 ln -s ${f} $file_for_processing; 46 ln -s ${f} $file_for_processing;
47 ##echo $is_fastq_file;
45 #end if 48 #end if
46 #end for 49 #end for
47 #if 'SingleEndFastqManifestPhred' in str($inputformat): 50 #if 'SingleEndFastqManifestPhred' in str($inputformat):
48 #set $cwd = str($outputpath.extra_files_path) + "_manifest_file.txt" 51 #set $cwf = str($outputpath.extra_files_path) + "_manifest_file.txt"
49 #set $m_file = open(str($cwd), 'w') 52 #set $tt = str("sample-id,absolute-filepath,direction")
50 $m_file.write("sample-id,absolute-filepath,direction\n") 53 echo $tt >> $cwf;
51 #for $f in $input_type.list_list: 54 #for $f in $input_type.list_list:
52 $m_file.write(str($f.name).split("_")[0]+",$PWD/input/"+str($f.name)+".gz,forward\n") 55 #set $tt = str($f.name).split("_")[0]+",$PWD/input/"+str($f.name).split(".")[0]+".fastq.gz,forward\n"
56 echo $tt >> $cwf;
53 #end for 57 #end for
54 $m_file.close() 58
55 #set $in_= str($cwd) 59 #set $in_= str($cwf)
56 #end if 60 #end if
57 61
58 62
59 #elif $input_type.type == 'list_paired_collection': 63 #elif $input_type.type == 'list_paired_collection':
60 64
61 #set $cwd = str($outputpath.extra_files_path) + "_manifest_file.txt" 65 #set $cwf = str($outputpath.extra_files_path) + "_manifest_file.txt"
62 #set $m_file = open(str($cwd), 'w') 66 #set $tt = str("sample-id,absolute-filepath,direction")
63 $m_file.write("sample-id,absolute-filepath,direction\n") 67 echo $tt >> $cwf;
64 68
65 #for $pair in $input_type.list_paired_collection: 69 #for $pair in $input_type.list_paired_collection:
66 #set $forward_is_fastq_file = $is_fastq(str($pair.forward)) 70 #set $forward_is_fastq_file = $is_fastq(str($pair.forward))
67 #set $reverse_is_fastq_file = $is_fastq(str($pair.reverse)) 71 #set $reverse_is_fastq_file = $is_fastq(str($pair.reverse))
68 72
69 #if $forward_is_fastq_file: 73 #if $forward_is_fastq_file:
70 gzip -c ${pair.forward} > input/${pair.name}_R1_001.fastq.gz; 74 gzip -c ${pair.forward} > input/${pair.name}_R1_001.fastq.gz;
71 $m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n") 75 #set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n"
76 echo $tt >> $cwf;
72 #else 77 #else
73 ln -s ${pair.forward} input/${pair.name}_R1_001.fastq.gz; 78 ln -s ${pair.forward} input/${pair.name}_R1_001.fastq.gz;
74 $m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n") 79 #set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R1_001.fastq.gz,forward\n"
80 echo $tt >> $cwf;
75 #end if 81 #end if
76 82
77 #if $reverse_is_fastq_file: 83 #if $reverse_is_fastq_file:
78 gzip -c ${pair.reverse} > input/${pair.name}_R2_001.fastq.gz; 84 gzip -c ${pair.reverse} > input/${pair.name}_R2_001.fastq.gz;
79 $m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n") 85 #set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n"
86 echo $tt >> $cwf;
80 #else 87 #else
81 ln -s ${pair.reverse} input/${pair.name}_R2_001.fastq.gz; 88 ln -s ${pair.reverse} input/${pair.name}_R2_001.fastq.gz;
82 $m_file.write(str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n") 89 #set $tt = str($pair.name).split("_")[0]+",$PWD/input/"+str($pair.name)+"_R2_001.fastq.gz,reverse\n"
90 echo $tt >> $cwf;
83 #end if 91 #end if
84 #end for 92 #end for
85 93
86 94
87 $m_file.close() 95
88 #if 'PairedEndFastqManifestPhred' in str($inputformat): 96 #if 'PairedEndFastqManifestPhred' in str($inputformat) or 'SingleEndFastqManifestPhred33V2' in str($inputformat) or 'SingleEndFastqManifestPhred33' in str($inputformat):
89 #set $in_= str($cwd) 97
98 #set $in_= str($cwf)
99
90 #elif 'Casava' in str($inputformat): 100 #elif 'Casava' in str($inputformat):
91 #set $in_= 'input' 101 #set $in_= 'input'
92 #end if 102 #end if
93 103
104
94 #else 105 #else
95 #set $res = $is_fastq(str($file)) 106 #set $res = $is_fastq(str($file))
96 107
97 #if $res 108 #if $res
98 gzip -c ${file} > ${file.name}.gz; 109 gzip -c ${file} > ${file.name}.gz;
266 </param> 277 </param>
267 </inputs> 278 </inputs>
268 <outputs> 279 <outputs>
269 <data format="qza" label="${tool.name} on ${on_string}: outputpath.qza" name="outputpath"/> 280 <data format="qza" label="${tool.name} on ${on_string}: outputpath.qza" name="outputpath"/>
270 </outputs> 281 </outputs>
271 <stdio> 282 <!--<stdio>
272 <exit_code range="2" level="warning" description="Error" /> 283 <exit_code range="2" level="warning" description="Error" />
273 </stdio> 284 </stdio>-->
274 <help> 285 <help>
275 </help> 286 </help>
276 <macros> 287 <macros>
277 <import>qiime_citation.xml</import> 288 <import>qiime_citation.xml</import>
278 </macros> 289 </macros>