annotate macros.xml @ 0:7004279ff8b7 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
author iuc
date Sun, 23 Jan 2022 21:34:54 +0000
parents
children 579ce63791e8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
1 <macros>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
2 <token name="@TOOL_VERSION@">3.15.3</token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
3 <token name="@VERSION_SUFFIX@">0</token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
4 <xml name="requirements">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
5 <requirements>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
6 <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
7 <requirement type="package" version="3.0">zip</requirement>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
8 <yield/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
9 </requirements>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
10 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
11 <xml name="stdio">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
12 <stdio>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
13 <exit_code range="1:"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
14 <regex match="Cannot allocate memory"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
15 source="stdout"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
16 level="fatal_oom"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
17 description="Out of memory error occurred"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
18 <regex match="The reads contain too many k-mers to fit into available memory"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
19 source="stdout"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
20 level="fatal_oom"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
21 description="Out of memory error occurred"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
22 </stdio>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
23 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
24 <xml name="version_command">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
25 <version_command><![CDATA[spades.py --version 2>&1 | awk -F 'v' '{print $2}']]></version_command>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
26 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
27 <token name="@INTYPES@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
28
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
29 </token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
30 <xml name="citations">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
31 <citations>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
32 <citation type="doi">10.1093/bioinformatics/btv688</citation>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
33 <citation type="doi">10.1093/bioinformatics/btu266</citation>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
34 <citation type="doi">10.1093/bioinformatics/btv337</citation>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
35 <yield/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
36 </citations>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
37 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
38 <xml name="operation_mode" token_help="">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
39 <param name="operation_mode" type="select" label="Operation mode" help="@HELP@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
40 <option value="">Assembly and error correction</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
41 <option value="--only-assembler">Only assembler (--only-assembler)</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
42 <option value="--only-error-correction">Only error correction (--only-error-correction)</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
43 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
44 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
45
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
46
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
47 <!-- PREPARE INPUT FILES-->
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
48
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
49 <token name="@PREPROCESS_INPUT_FILES_MAIN@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
50 #if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
51 mkdir -p reads1 &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
52 #set file_paths1 = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
53 #for $input_file in $singlePaired.input1
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
54 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
55 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
56 #set $file_path = 'reads1/' + $fname
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
57 ln -s '$input_file' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
58 $file_paths1.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
59 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
60 #else if $singlePaired.sPaired == "paired"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
61 mkdir -p paired_reads1 &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
62 #set fw_reads1 = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
63 #for $input_file in $singlePaired.input1
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
64 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
65 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
66 #set $file_path = 'paired_reads1/' + str($fname)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
67 ln -s '$input_file' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
68 $fw_reads1.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
69 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
70 #set rv_reads1 = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
71 #for $input_file in $singlePaired.input2
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
72 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
73 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
74 #set $file_path = 'paired_reads1/' + str($fname)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
75 ln -s '$input_file' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
76 $rv_reads1.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
77 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
78 #silent $fw_reads1.sort()
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
79 #silent $rv_reads1.sort()
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
80 #else
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
81 mkdir -p paired_reads1 &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
82 #set fw_reads1 = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
83 #set rv_reads1 = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
84 #for $i, $input_file in enumerate($singlePaired.input)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
85 #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
86 #set $file_path = 'paired_reads1/fw' + str($i) + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
87 ln -s '$input_file.forward' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
88 $fw_reads1.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
89 #set $file_path = 'paired_reads1/rv' + str($i) + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
90 ln -s '$input_file.reverse' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
91 $rv_reads1.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
92 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
93 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
94 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
95
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
96 <token name="@PREPROCESS_INPUT_FILES_ADDITIONAL@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
97 #if $additional_reads.singlePaired.sPaired == "single" or $additional_reads.singlePaired.sPaired == "paired_interlaced"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
98 mkdir -p reads2 &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
99 #set file_paths2 = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
100 #for $input_file in $additional_reads.singlePaired.input1
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
101 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
102 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
103 #set $file_path = 'reads2/' + $fname
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
104 ln -s '$input_file' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
105 $file_paths2.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
106 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
107 #else if $additional_reads.singlePaired.sPaired == "paired"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
108 mkdir -p paired_reads2 &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
109 #set fw_reads2 = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
110 #for $input_file in $additional_reads.singlePaired.input1
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
111 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
112 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
113 #set $file_path = 'paired_reads2/' + str($fname)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
114 ln -s '$input_file' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
115 $fw_reads2.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
116 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
117 #set rv_reads2 = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
118 #for $input_file in $additional_reads.singlePaired.input2
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
119 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
120 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
121 #set $file_path = 'paired_reads2/' + str($fname)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
122 ln -s '$input_file' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
123 $rv_reads2.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
124 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
125 #silent $fw_reads2.sort()
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
126 #silent $rv_reads2.sort()
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
127 #else
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
128 mkdir -p paired_reads2 &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
129 #set fw_reads2 = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
130 #set rv_reads2 = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
131 #for $i, $input_file in enumerate($additional_reads.singlePaired.input)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
132 #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
133 #set $file_path = 'paired_reads2/fw' + str($i) + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
134 ln -s '$input_file.forward' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
135 $fw_reads2.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
136 #set $file_path = 'paired_reads2/rv' + str($i) + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
137 ln -s '$input_file.reverse' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
138 $rv_reads2.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
139 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
140 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
141 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
142
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
143 <!-- COMMANDS -->
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
144
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
145 <token name="@RESOURCES@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
146 -t \${GALAXY_SLOTS:-4}
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
147 -m \${GALAXY_MEMORY_GB:-8}
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
148 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
149
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
150 <token name="@INPUT_READS_MAIN@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
151 #if $singlePaired.sPaired == "single"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
152 #for $read in $file_paths1
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
153 --s $library '${read}'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
154 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
155 #else if $singlePaired.sPaired == "paired"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
156 #for $read in $fw_reads1
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
157 --${singlePaired.type_paired}-1 $library '${read}'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
158 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
159 #for $read in $rv_reads1
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
160 --${singlePaired.type_paired}-2 $library '${read}'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
161 --${singlePaired.type_paired}-or $library $singlePaired.orientation
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
162 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
163 #else if $singlePaired.sPaired == "paired_interlaced"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
164 #for $read in $file_paths1
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
165 --${singlePaired.type_paired}-12 $library '${read}'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
166 --${singlePaired.type_paired}-or $library $singlePaired.orientation
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
167 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
168 #else
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
169 #for $read in $fw_reads1
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
170 --${singlePaired.type_paired}-1 $library '${read}'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
171 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
172 #for $read in $rv_reads1
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
173 --${singlePaired.type_paired}-2 $library '${read}'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
174 --${singlePaired.type_paired}-or $library $singlePaired.orientation
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
175 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
176 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
177 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
178
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
179
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
180 <token name="@INPUT_READS_ADDITIONAL@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
181 @LIBRARY_NUMBER@
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
182 #if $additional_reads.singlePaired.sPaired == "single"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
183 #for $read in $file_paths2
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
184 --s $library '${read}'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
185 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
186 #else if $additional_reads.singlePaired.sPaired == "paired"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
187 #for $read in $fw_reads2
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
188 --${additional_reads.singlePaired.type_paired}-1 $library '${read}'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
189 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
190 #for $read in $rv_reads2
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
191 --${additional_reads.singlePaired.type_paired}-2 $library '${read}'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
192 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
193 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
194 #else if $additional_reads.singlePaired.sPaired == "paired_interlaced"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
195 #for $read in $file_paths2
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
196 --${additional_reads.singlePaired.type_paired}-12 $library '${read}'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
197 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
198 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
199 #else
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
200 #for $read in $fw_reads2
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
201 --${additional_reads.singlePaired.type_paired}-1 $library '${read}'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
202 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
203 #for $read in $rv_reads2
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
204 --${additional_reads.singlePaired.type_paired}-2 $library '${read}'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
205 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
206 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
207 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
208 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
209
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
210 <token name="@PIPELINE_OPTIONS@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
211 #for $i in $mode_sel
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
212 $i
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
213 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
214 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
215
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
216 <token name="@KMER@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
217 #if $kmer_cond.kmer_sel != 'auto'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
218 -k '$kmer_cond.manual'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
219 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
220 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
221
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
222 <token name="@PHREDOFFSET@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
223 #if $phred_offset != 'auto'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
224 --phred-offset $phred_offset
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
225 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
226 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
227
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
228 <!-- ADDITIONAL INPUTS-->
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
229
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
230 <token name="@PREPROCESS_CONTIGS_FILES@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
231 #if $arf.trusted_contigs
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
232 mkdir -p trusted_contigs &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
233 #set trusted_contigs = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
234 #for $i, $input_file in enumerate($arf.trusted_contigs,1)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
235 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
236 #set $fname = 'file' + str($i) + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
237 #set $file_path = 'trusted_contigs/' + $fname
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
238 ln -s '$input_file' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
239 $trusted_contigs.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
240 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
241 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
242 #if $arf.untrusted_contigs
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
243 mkdir -p untrusted_contigs &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
244 #set untrusted_contigs = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
245 #for $i, $input_file in enumerate($arf.untrusted_contigs,1)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
246 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
247 #set $fname = 'file' + str($i) + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
248 #set $file_path = 'untrusted_contigs/' + $fname
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
249 ln -s '$input_file' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
250 $untrusted_contigs.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
251 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
252 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
253 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
254
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
255 <token name="@PREPROCESS_NANOPORE_PACBIO_FILES@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
256 #if $arf.nanopore
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
257 mkdir -p nanopore_reads &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
258 #set nanopore_reads = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
259 #for $i, $input_file in enumerate($arf.nanopore,1)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
260 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
261 #set $fname = 'file' + str($i) + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
262 #set $file_path = 'nanopore_reads/' + $fname
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
263 ln -s '$input_file' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
264 $nanopore_reads.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
265 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
266 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
267 #if $arf.pacbio
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
268 mkdir -p pacbio_reads &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
269 #set pacbio_reads = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
270 #for $i, $input_file in enumerate($arf.pacbio,1)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
271 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
272 #set $fname = 'file' + str($i) + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
273 #set $file_path = 'pacbio_reads/' + $fname
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
274 ln -s '$input_file' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
275 $pacbio_reads.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
276 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
277 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
278 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
279
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
280 <token name="@PREPROCESS_SANGER_FILES@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
281 #if $arf.sanger
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
282 mkdir -p sanger_reads &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
283 #set sanger_reads = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
284 #for $i, $input_file in enumerate($arf.sanger,1)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
285 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
286 #set $fname = 'file' + str($i) + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
287 #set $file_path = 'sanger_reads/' + $fname
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
288 ln -s '$input_file' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
289 $sanger_reads.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
290 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
291 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
292 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
293
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
294 <token name="@PREPROCESS_FL_RNA_FILES@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
295 #if $arf.flrna
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
296 mkdir -p flrna_reads &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
297 #set flrna_reads = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
298 #for $i, $input_file in enumerate($arf.flrna,1)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
299 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
300 #set $fname = 'file' + str($i) + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
301 #set $file_path = 'flrna_reads/' + $fname
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
302 ln -s '$input_file' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
303 $flrna_reads.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
304 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
305 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
306 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
307
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
308 <token name="@PREPROCESS_ASSEMBLY_GRAPH_FILES@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
309 #if $arf.assembly_graph
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
310 mkdir -p assembly_graphs &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
311 #set assembly_graphs = []
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
312 #for $i, $input_file in enumerate($arf.assembly_graph,1)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
313 #set $ext = $input_file.ext.replace('gfa1', 'gfa')
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
314 #set $fname = 'file' + str($i) + '.' + $ext
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
315 #set $file_path = 'assembly_graphs/' + $fname
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
316 ln -s '$input_file' $file_path &&
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
317 $assembly_graphs.append($file_path)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
318 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
319 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
320 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
321
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
322
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
323 <token name="@NANOPORE_PACBIO@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
324 #if $arf.nanopore
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
325 #for $read in $nanopore_reads
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
326 --nanopore $read
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
327 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
328 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
329 #if $arf.pacbio
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
330 #for $read in $pacbio_reads
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
331 --pacbio $read
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
332 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
333 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
334 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
335
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
336
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
337 <token name="@SANGER@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
338 #if $arf.sanger
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
339 #for $read in $sanger_reads
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
340 --sanger $read
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
341 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
342 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
343 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
344
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
345 <token name="@FL_RNA@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
346 #if $arf.flrna
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
347 #for $read in $flrna_reads
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
348 --fl-rna $read
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
349 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
350 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
351 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
352
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
353 <token name="@ASSEMBLY_GRAPH@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
354 #if $arf.assembly_graph
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
355 #for $graph in $assembly_graphs
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
356 --assembly-graph $graph
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
357 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
358 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
359 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
360
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
361 <token name="@CONTIGS@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
362 #if $arf.trusted_contigs
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
363 #for $read in $trusted_contigs
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
364 --trusted-contigs $read
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
365 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
366 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
367 #if $arf.untrusted_contigs
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
368 #for $read in $untrusted_contigs
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
369 --untrusted-contigs $read
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
370 #end for
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
371 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
372 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
373
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
374 <token name="@LIBRARY_NUMBER@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
375 #if $additional_reads.selector == 'true' and $additional_reads.library_number == 'false'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
376 #set $library += 1
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
377 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
378 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
379
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
380 <!-- POSTPROCESSING -->
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
381
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
382 <token name="@STATS@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
383 #if 'cs' in $optional_output
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
384 && test -f 'output/contigs.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/contigs.fasta' > '$out_cs' || echo 'No contigs.fasta.'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
385 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
386 #if 'ss' in $optional_output
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
387 && test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' || echo 'No scaffolds.fasta.'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
388 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
389 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
390
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
391 <token name="@CORRECTED@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
392 #if 'corrected' in $optional_output
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
393 && test -d 'output/corrected' && zip -q -r 'corrected.zip' 'output/corrected/*.fastq.gz' || echo 'No output files for corrected reads.'
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
394 #end if
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
395 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
396
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
397 <!--
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
398 input
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
399 -->
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
400
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
401 <xml name="input_files_all" token_format="" token_label="" token_help="It assumes that all samples belong to the same library. If you want to use samples from two different libraries, include the second library as additional set of short-reads.">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
402 <conditional name="singlePaired">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
403 <param name="sPaired" type="select" label="Single-end or paired-end short-reads" help="@HELP@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
404 <option value="single" selected="true">Single-end</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
405 <option value="paired">Paired-end: individual datasets</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
406 <option value="paired_interlaced">Paired-end: interlaced reads</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
407 <option value="paired_collection">Paired-end: list of dataset pairs</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
408 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
409 <when value="single">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
410 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
411 </when>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
412 <when value="paired">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
413 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: forward reads"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
414 <param format="@FORMAT@" name="input2" type="data" multiple="true" label="@LABEL@: reverse reads"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
415 <expand macro="type_paired"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
416 <expand macro="orientation"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
417 </when>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
418 <when value="paired_interlaced">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
419 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
420 <expand macro="type_paired"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
421 <expand macro="orientation"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
422 </when>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
423 <when value="paired_collection">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
424 <param format="@FORMAT@" name="input" type="data_collection" collection_type="list:paired" label="@LABEL@: collection"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
425 <expand macro="type_paired"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
426 <expand macro="orientation"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
427 </when>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
428 </conditional>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
429 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
430
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
431 <xml name="input_files_paired" token_format="" token_label="" token_help="It assumes that all samples belong to the same library. If you want to use samples from two different libraries, include the second library as additional set of short-reads.">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
432 <conditional name="singlePaired">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
433 <param name="sPaired" type="select" label="Pair-end reads input format" help="@HELP@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
434 <option value="paired" selected="true">Paired-end: individual datasets</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
435 <option value="paired_interlaced">Paired-end: interlaced reads</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
436 <option value="paired_collection">Paired-end: list of dataset pairs</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
437 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
438 <when value="paired">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
439 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: forward reads"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
440 <param format="@FORMAT@" name="input2" type="data" multiple="true" label="@LABEL@: reverse reads"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
441 <expand macro="type_paired"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
442 <expand macro="orientation"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
443 </when>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
444 <when value="paired_interlaced">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
445 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
446 <expand macro="type_paired"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
447 <expand macro="orientation"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
448 </when>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
449 <when value="paired_collection">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
450 <param format="@FORMAT@" name="input" type="data_collection" collection_type="list:paired" label="@LABEL@: collection"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
451 <expand macro="type_paired"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
452 <expand macro="orientation"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
453 </when>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
454 </conditional>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
455 <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the same sample, it means that they belong to the same library.">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
456 <option value="true" selected="true">True</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
457 <option value="false">False</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
458 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
459 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
460
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
461 <xml name="orientation">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
462 <param name="orientation" type="select" label="Select orientation of reads" help="Note: mate-pair fragments are generally in a RF conformation. In general, paired-end reads tend to be in a FR orientation.">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
463 <option value="fr" selected="true"><![CDATA[FR (-> <-)]]></option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
464 <option value="rf"><![CDATA[RF (<- ->)]]></option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
465 <option value="ff"><![CDATA[FF (-> ->)]]></option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
466 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
467 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
468
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
469 <xml name="type_paired">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
470 <param name="type_paired" type="select" label="Type of paired-reads"
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
471 help="In paired-end sequencing, the library preparation yields a set of fragments, and the machine sequences each fragment from both ends. In mate-pair sequencing,
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
472 the library preparation yields two fragments that are distal to each other in the genome and in the opposite in orientation to that of a mate-paired fragment.">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
473 <option value="pe" selected="true">Default (--pe)</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
474 <option value="mp">Mate-pair reads (--mp)</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
475 <option value="hqmp">High-quality Nextera mate-pair reads (--hqmp)</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
476 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
477 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
478
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
479 <xml name="input_additional_files_all" token_format="" token_label="" token_help="">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
480 <conditional name="additional_reads">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
481 <param name="selector" type="select" label="Use an additional set of short-reads" help="Enable this option if you want to combine to data sources (e.g. single and paired reads).">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
482 <option value="false" selected="true">Disabled</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
483 <option value="true">Enabled</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
484 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
485 <when value="true">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
486 <expand macro="input_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)" help="@HELP@"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
487 <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the sample sample, it means that they belong to the same library.">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
488 <option value="true" selected="true">True</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
489 <option value="false">False</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
490 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
491 </when>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
492 <when value="false"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
493 </conditional>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
494 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
495
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
496 <xml name="input_additional_files_paired" token_format="" token_label="" token_help="" >
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
497 <conditional name="additional_reads">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
498 <param name="selector" type="select" label="Use an additional set of short-reads" help="Enable this option if you want to combine to data sources (e.g. single and paired reads).">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
499 <option value="false" selected="true">Disabled</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
500 <option value="true">Enabled</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
501 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
502 <when value="true">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
503 <expand macro="input_files_paired" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)" help="@HELP@"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
504 <param name="library_number" type="select" label="The samples belong to the same library" help="If the reads have been generated from the sample sample, it means that they belong to the same library.">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
505 <option value="true" selected="true">True</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
506 <option value="false">False</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
507 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
508 </when>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
509 <when value="false"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
510 </conditional>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
511 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
512
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
513 <xml name="covcutoff">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
514 <conditional name="cov_cond">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
515 <param argument="--cov-cutoff" type="select" label="Set coverage cutoff option" help="When set to 'auto' SPAdes automatically computes coverage threshold using conservative strategy">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
516 <option value="off">Off</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
517 <option value="auto">Auto</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
518 <option value="value">User specific</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
519 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
520 <when value="off"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
521 <when value="auto"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
522 <when value="value">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
523 <param name="manual" type="float" min="0" value="" label="Set value"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
524 </when>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
525 </conditional>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
526 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
527 <xml name="pipeline_options">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
528 <param name="mode_sel" type="select" label="Pipeline options" multiple="true" optional="true" display="checkboxes" help="Error correction requires FASTQ input files.">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
529 <option value="--disable-rr">Disable repeat resolution (--disable-rr)</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
530 <yield/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
531 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
532 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
533 <xml name="kmer" token_help="" token_default="21,33,55,77">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
534 <conditional name="kmer_cond">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
535 <param name="kmer_sel" argument="-k" type="select" label="Select k-mer detection option" help="@HELP@ Comma-separated list, all values must be odd, less than 128 and listed in ascending order.">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
536 <option value="auto">Auto</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
537 <option value="manual">User specific</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
538 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
539 <when value="auto"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
540 <when value="manual">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
541 <param name="manual" type="text" value="@DEFAULT@" label="K-mer size values" help="List of k-mer sizes (must be odd and less than 128)">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
542 <sanitizer invalid_char="">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
543 <valid initial="string.digits">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
544 <add value="," />
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
545 </valid>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
546 </sanitizer>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
547 <validator type="regex">[0-9,]+</validator>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
548 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
549 </when>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
550 </conditional>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
551 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
552 <xml name="nanopore_pacbio">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
553 <param argument="--nanopore" type="data" format="fastq,fastq.gz" multiple="true" optional="true" label="Nanopore reads" help="SPAdes will use Oxford Nanopore reads for gap closure and repeat resolution"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
554 <param argument="--pacbio" type="data" format="fastq,fastq.gz" multiple="true" optional="true" label="PacBio CLR reads" help="It is not recommended to run SPAdes on PacBio reads with low coverage (less than 5). In addition, SPAdes develpers suggest not to run SPAdes on PacBio reads for large genomes. SPAdes will use PacBio CLR reads for gap closure and repeat resolution"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
555 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
556 <xml name="flrna">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
557 <param argument="--fl-rna" name="flrna" type="data" format="fastq,fastq.gz,fasta,fasta.gz,fastqsanger,fastqsanger.gz" multiple="true" optional="true" label="PacBio/Nanopore/contigs that capture full-length transcripts" help="In addition to long reads, you may also provide a separate file with reads capturing the entire transcript sequences using this option. Full-length transcripts in such reads can be typically detected using the adapters. Note, that FL reads should be trimmed so that the adapters are excluded."/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
558 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
559
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
560 <xml name="phred">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
561 <param argument="--phred-offset" type="select" label="Set Phred quality offset" help="Phred quality offset in the input reads. Default: auto-detect">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
562 <option value="auto" selected="true">Auto</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
563 <option value="33">33 (Sanger)</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
564 <option value="64">64 (Illumina)</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
565 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
566 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
567 <xml name="reads" token_paramname="reads" token_help="" token_label="">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
568 <param name="@PARAMNAME@" type="data" format="fastq,fastq.gz" label="@LABEL@ reads" help="@HELP@"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
569 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
570 <xml name="sanger">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
571 <param argument="--sanger" type="data" format="fastq,fastq.gz" multiple="true" optional="true" label="Sanger reads"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
572 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
573 <xml name="contigs">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
574 <param argument="--trusted-contigs" type="data" format="fasta,fasta.gz" multiple="true" optional="true" label="Trusted contigs" help="Reliable contigs of the same genome, which are likely to have no misassemblies and small rate of other errors (e.g. mismatches and indels). This option is not intended for contigs of the related species."/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
575 <param argument="--untrusted-contigs" type="data" format="fasta,fasta.gz" multiple="true" optional="true" label="Untrusted contigs" help="Contigs of the same genome, quality of which is average or unknown. Contigs of poor quality can be used but may introduce errors in the assembly. This option is also not intended for contigs of the related species."/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
576 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
577 <xml name="assembly_graph">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
578 <param argument="--assembly-graph" type="data" format="gfa1" multiple="true" optional="true" label="Assembly graphs" help=" The primary purpose of this option to run these pipelines on already constructed and simplified assembly graph this way skipping a large part of SPAdes pipeline."/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
579 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
580 <xml name="optional_output">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
581 <param name="optional_output" type="select" multiple="true" optional="false" label="Select optional output file(s)" help="Only shown in history if selected here and generated by the specific run.">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
582 <option value="ag" selected="true">Assembly graph</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
583 <option value="ags" selected="true">Assembly graph with scaffolds</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
584 <option value="cn" selected="true">Contigs</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
585 <option value="cp">Contigs paths</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
586 <option value="cr">Corrected reads</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
587 <option value="cs">Contigs stats</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
588 <option value="l">Log</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
589 <option value="sc" selected="true">Scaffolds</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
590 <option value="sp">Scaffolds paths</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
591 <option value="ss">Scaffolds stats</option>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
592 </param>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
593 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
594 <!--
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
595 output
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
596 -->
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
597
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
598 <xml name="out_ag">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
599 <data name="out_ag" format="fastg" from_work_dir="output/assembly_graph.fastg" label="${tool.name} on ${on_string}: Assembly graph">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
600 <filter>'ag' in optional_output</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
601 <filter> operation_mode != '--only-error-correction'</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
602 </data>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
603 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
604 <xml name="out_ags">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
605 <data name="out_ags" format="txt" from_work_dir="output/assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: Assembly graph with scaffolds">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
606 <filter>'ags' in optional_output</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
607 <filter> operation_mode != '--only-error-correction'</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
608 </data>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
609 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
610 <xml name="out_cn">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
611 <data name="out_cn" format="fasta" from_work_dir="output/contigs.fasta" label="${tool.name} on ${on_string}: Contigs">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
612 <filter>'cn' in optional_output</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
613 <filter> operation_mode != '--only-error-correction'</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
614 </data>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
615 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
616 <xml name="out_cp">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
617 <data name="out_cp" format="txt" from_work_dir="output/contigs.paths" label="${tool.name} on ${on_string}: Contigs paths">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
618 <filter>'cp' in optional_output</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
619 <filter> operation_mode != '--only-error-correction'</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
620 </data>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
621 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
622 <xml name="out_cr">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
623 <!-- some mode combinations create fastq, some fasta -->
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
624 <collection name="out_cr" type="list" label="${tool.name} on ${on_string}: Corrected reads">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
625 <filter>'cr' in optional_output</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
626 <filter> operation_mode != '--only-assembler'</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
627 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastq\.gz" format="fastq" directory="output/corrected"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
628 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta\.gz" format="fasta" directory="output/corrected"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
629 </collection>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
630 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
631 <xml name="out_cs">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
632 <data name="out_cs" format="tabular" label="${tool.name} on ${on_string}: Contigs stats">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
633 <actions>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
634 <action name="column_names" type="metadata" default="name,length,coverage"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
635 </actions>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
636 <filter>'cs' in optional_output</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
637 <filter> operation_mode != '--only-error-correction'</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
638 </data>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
639 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
640 <xml name="out_l">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
641 <data name="out_l" format="txt" from_work_dir="output/spades.log" label="${tool.name} on ${on_string}: Log">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
642 <filter>'l' in optional_output</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
643 </data>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
644 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
645 <xml name="out_sc">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
646 <data name="out_sc" format="fasta" from_work_dir="output/scaffolds.fasta" label="${tool.name} on ${on_string}: Scaffolds">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
647 <filter>'sc' in optional_output</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
648 <filter> operation_mode != '--only-error-correction'</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
649 </data>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
650 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
651 <xml name="out_sp">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
652 <data name="out_sp" format="txt" from_work_dir="output/scaffolds.paths" label="${tool.name} on ${on_string}: Scaffolds paths">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
653 <filter>'sp' in optional_output</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
654 <filter> operation_mode != '--only-error-correction'</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
655 </data>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
656 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
657 <xml name="out_ss">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
658 <data name="out_ss" format="tabular" label="${tool.name} on ${on_string}: Scaffolds stats">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
659 <actions>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
660 <action name="column_names" type="metadata" default="name,length,coverage"/>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
661 </actions>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
662 <filter>'ss' in optional_output</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
663 <filter> operation_mode != '--only-error-correction'</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
664 </data>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
665 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
666 <xml name="out_rs">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
667 <data name="out_rs" format="fasta" from_work_dir="output/raw_scaffolds.fasta" label="${tool.name} on ${on_string}: Raw scaffolds">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
668 <filter>'rs' in optional_output</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
669 </data>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
670 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
671 <xml name="out_b">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
672 <data name="out_b" format="txt" from_work_dir="output/hmm_statistics.txt" label="${tool.name} on ${on_string}: HMM statistics">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
673 <filter>'b' in optional_output</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
674 </data>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
675 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
676 <xml name="out_dg">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
677 <data name="out_dg" format="fasta" from_work_dir="output/domain_graph.dot" label="${tool.name} on ${on_string}: Domain graph">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
678 <filter>'dg' in optional_output</filter>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
679 </data>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
680 </xml>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
681 <!--
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
682 help
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
683 -->
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
684
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
685 <token name="@HELP_IN@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
686
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
687 SPAdes takes as input paired-end reads, mate-pairs and single (unpaired) reads in FASTA and FASTQ. For IonTorrent data SPAdes also supports unpaired reads in unmapped BAM format (like the one produced by Torrent Server). However, in order to run read error correction, reads should be in FASTQ or BAM format. Sanger, Oxford Nanopore and PacBio CLR reads can be provided in both formats since SPAdes does not run error correction for these types of data.
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
688
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
689 To run SPAdes 3.15.3 you need at least one library of the following types:
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
690
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
691 - Illumina paired-end/high-quality mate-pairs/unpaired reads
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
692 - IonTorrent paired-end/high-quality mate-pairs/unpaired reads
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
693 - PacBio CCS reads
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
694 - Illumina and IonTorrent libraries should not be assembled together. All other types of input data are compatible. SPAdes should not be used if only PacBio CLR, Oxford Nanopore, Sanger reads or additional contigs are available.
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
695
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
696 SPAdes supports mate-pair only assembly. However, we recommend to use only high-quality mate-pair libraries in this case (e.g. that do not have a paired-end part). We tested mate-pair only pipeline using Illumina Nextera mate-pairs.
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
697
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
698 Notes:
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
699
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
700 - It is strongly suggested to provide multiple paired-end and mate-pair libraries according to their insert size (from smallest to longest).
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
701 - It is not recommended to run SPAdes on PacBio reads with low coverage (less than 5).
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
702 - We suggest not to run SPAdes on PacBio reads for large genomes.
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
703 - SPAdes accepts gzip-compressed files.
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
704
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
705 A detailed description can be found in the `input section <https://github.com/ablab/spades/#sec3.1>`_ of the manual.
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
706 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
707 <token name="@HELP_OUT_AG@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
708 - Assembly graph
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
709 </token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
710 <token name="@HELP_OUT_AGS@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
711 - Assembly graph with scaffolds
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
712 </token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
713 <token name="@HELP_OUT_C@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
714 - Contigs
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
715 </token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
716 <token name="@HELP_OUT_CP@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
717 - Contigs paths in the assembly graph
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
718 </token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
719 <token name="@HELP_OUT_CS@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
720 - Contigs stats
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
721 </token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
722 <token name="@HELP_OUT_CR@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
723 - Corrected reads by BayesHammer
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
724 </token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
725 <token name="@HELP_OUT_L@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
726 - Log file
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
727 </token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
728 <token name="@HELP_OUT_S@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
729 - Scaffolds (recommended for use as resulting sequences)
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
730 </token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
731 <token name="@HELP_OUT_SP@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
732 - Scaffolds paths in the assembly graph
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
733 </token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
734 <token name="@HELP_OUT_SS@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
735 - Scaffolds stats
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
736 </token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
737 <token name="@HELP_WID@">
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
738 SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
739 </token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
740 <token name="@IONTORRENT@"><![CDATA[
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
741 The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our `recommendation for long reads <https://cab.spbu.ru/files/release3.12.0/manual.html#sec3.4>`_ (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o <previous_output_dir>. Do not forget to copy contigs and scaffolds from the previous run. We're planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions.
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
742
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
743 You may need no error correction for Hi-Q enzyme at all. However, we suggest trying to assemble your data with and without error correction and select the best variant.
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
744
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
745 For non-trivial datasets (e.g. with high GC, low or uneven coverage) we suggest to enable single-cell mode (setting --sc option) and use k-mer lengths of 21,33,55.
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
746
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
747 ]]></token>
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
748
7004279ff8b7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
749 </macros>