Mercurial > repos > iuc > spades_rnaviralspades

annotate macros.xml @ 8:de1260f8a300 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 066e075c1599b29e92708194db2b2ccc30b7677c
author iuc
date Mon, 12 Feb 2024 21:45:41 +0000
parents d5fb354f745d
children 6357b127161e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
1 <macros>
8
de1260f8a300 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 066e075c1599b29e92708194db2b2ccc30b7677c
iuc
parents: 7
diff changeset
2 <token name="@TOOL_VERSION@">3.15.5</token>
de1260f8a300 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 066e075c1599b29e92708194db2b2ccc30b7677c
iuc
parents: 7
diff changeset
3 <token name="@VERSION_SUFFIX@">1</token>
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
4 <xml name="requirements">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
5 <requirements>
5df83f4bad67 "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>
5df83f4bad67 "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>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
8 <yield/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
9 </requirements>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
10 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
11 <xml name="stdio">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
12 <stdio>
5df83f4bad67 "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:"/>
5df83f4bad67 "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"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
15 source="stdout"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
16 level="fatal_oom"
5df83f4bad67 "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"/>
5df83f4bad67 "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"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
19 source="stdout"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
20 level="fatal_oom"
5df83f4bad67 "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"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
22 </stdio>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
23 </xml>
5df83f4bad67 "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">
5df83f4bad67 "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>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
26 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
27 <token name="@INTYPES@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
28
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
29 </token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
30 <xml name="citations">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
31 <citations>
5df83f4bad67 "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>
5df83f4bad67 "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>
5df83f4bad67 "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>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
35 <yield/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
36 </citations>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
37 </xml>
5df83f4bad67 "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="">
5df83f4bad67 "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@">
5df83f4bad67 "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>
5df83f4bad67 "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>
5df83f4bad67 "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>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
43 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
44 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
45
6
48cf45a53456 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
iuc
parents: 5
diff changeset
46 <token name="@OMP_THREADS@"><![CDATA[
48cf45a53456 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
iuc
parents: 5
diff changeset
47 export OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-4} &&
48cf45a53456 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
iuc
parents: 5
diff changeset
48 ]]></token>
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
49
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
50 <!-- PREPARE INPUT FILES-->
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
51
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
52 <token name="@PREPROCESS_INPUT_FILES_MAIN@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
53 #if $singlePaired.sPaired == "single" or $singlePaired.sPaired == "paired_interlaced"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
54 mkdir -p reads1 &&
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
55 #set file_paths1 = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
56 #for $input_file in $singlePaired.input1
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
57 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
58 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
59 #set $file_path = 'reads1/' + $fname
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
60 ln -s '$input_file' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
61 $file_paths1.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
62 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
63 #else if $singlePaired.sPaired == "paired"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
64 mkdir -p paired_reads1 &&
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
65 #set fw_reads1 = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
66 #for $input_file in $singlePaired.input1
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
67 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
68 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
69 #set $file_path = 'paired_reads1/' + str($fname)
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
70 ln -s '$input_file' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
71 $fw_reads1.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
72 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
73 #set rv_reads1 = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
74 #for $input_file in $singlePaired.input2
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
75 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
76 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
77 #set $file_path = 'paired_reads1/' + str($fname)
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
78 ln -s '$input_file' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
79 $rv_reads1.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
80 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
81 #silent $fw_reads1.sort()
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
82 #silent $rv_reads1.sort()
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
83 #else
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
84 mkdir -p paired_reads1 &&
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
85 #set fw_reads1 = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
86 #set rv_reads1 = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
87 #for $i, $input_file in enumerate($singlePaired.input)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
88 #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
89 #set $file_path = 'paired_reads1/fw' + str($i) + '.' + $ext
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
90 ln -s '$input_file.forward' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
91 $fw_reads1.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
92 #set $file_path = 'paired_reads1/rv' + str($i) + '.' + $ext
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
93 ln -s '$input_file.reverse' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
94 $rv_reads1.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
95 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
96 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
97 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
98
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
99 <token name="@PREPROCESS_INPUT_FILES_ADDITIONAL@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
100 #if $additional_reads.singlePaired.sPaired == "single" or $additional_reads.singlePaired.sPaired == "paired_interlaced"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
101 mkdir -p reads2 &&
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
102 #set file_paths2 = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
103 #for $input_file in $additional_reads.singlePaired.input1
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
104 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
105 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
106 #set $file_path = 'reads2/' + $fname
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
107 ln -s '$input_file' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
108 $file_paths2.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
109 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
110 #else if $additional_reads.singlePaired.sPaired == "paired"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
111 mkdir -p paired_reads2 &&
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
112 #set fw_reads2 = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
113 #for $input_file in $additional_reads.singlePaired.input1
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
114 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
115 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
116 #set $file_path = 'paired_reads2/' + str($fname)
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
117 ln -s '$input_file' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
118 $fw_reads2.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
119 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
120 #set rv_reads2 = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
121 #for $input_file in $additional_reads.singlePaired.input2
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
122 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
123 #set $fname = $input_file.element_identifier.replace(" ","_") + '.' + $ext
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
124 #set $file_path = 'paired_reads2/' + str($fname)
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
125 ln -s '$input_file' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
126 $rv_reads2.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
127 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
128 #silent $fw_reads2.sort()
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
129 #silent $rv_reads2.sort()
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
130 #else
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
131 mkdir -p paired_reads2 &&
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
132 #set fw_reads2 = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
133 #set rv_reads2 = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
134 #for $i, $input_file in enumerate($additional_reads.singlePaired.input)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
135 #set $ext = $input_file.forward.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
136 #set $file_path = 'paired_reads2/fw' + str($i) + '.' + $ext
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
137 ln -s '$input_file.forward' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
138 $fw_reads2.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
139 #set $file_path = 'paired_reads2/rv' + str($i) + '.' + $ext
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
140 ln -s '$input_file.reverse' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
141 $rv_reads2.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
142 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
143 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
144 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
145
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
146 <!-- COMMANDS -->
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
147
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
148 <token name="@RESOURCES@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
149 -t \${GALAXY_SLOTS:-4}
3
d159735a6a9f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit b7b09cff3ddcdf26f27aabfcf41a8ce0a3985d87"
iuc
parents: 1
diff changeset
150 -m \$((\${GALAXY_MEMORY_MB:-8192}/1024))
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
151 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
152
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
153 <token name="@INPUT_READS_MAIN@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
154 #if $singlePaired.sPaired == "single"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
155 #for $read in $file_paths1
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
156 --s $library '${read}'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
157 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
158 #else if $singlePaired.sPaired == "paired"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
159 #for $read in $fw_reads1
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
160 --${singlePaired.type_paired}-1 $library '${read}'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
161 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
162 #for $read in $rv_reads1
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
163 --${singlePaired.type_paired}-2 $library '${read}'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
164 --${singlePaired.type_paired}-or $library $singlePaired.orientation
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
165 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
166 #else if $singlePaired.sPaired == "paired_interlaced"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
167 #for $read in $file_paths1
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
168 --${singlePaired.type_paired}-12 $library '${read}'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
169 --${singlePaired.type_paired}-or $library $singlePaired.orientation
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
170 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
171 #else
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
172 #for $read in $fw_reads1
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
173 --${singlePaired.type_paired}-1 $library '${read}'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
174 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
175 #for $read in $rv_reads1
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
176 --${singlePaired.type_paired}-2 $library '${read}'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
177 --${singlePaired.type_paired}-or $library $singlePaired.orientation
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
178 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
179 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
180 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
181
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
182
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
183 <token name="@INPUT_READS_ADDITIONAL@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
184 @LIBRARY_NUMBER@
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
185 #if $additional_reads.singlePaired.sPaired == "single"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
186 #for $read in $file_paths2
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
187 --s $library '${read}'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
188 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
189 #else if $additional_reads.singlePaired.sPaired == "paired"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
190 #for $read in $fw_reads2
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
191 --${additional_reads.singlePaired.type_paired}-1 $library '${read}'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
192 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
193 #for $read in $rv_reads2
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
194 --${additional_reads.singlePaired.type_paired}-2 $library '${read}'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
195 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
196 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
197 #else if $additional_reads.singlePaired.sPaired == "paired_interlaced"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
198 #for $read in $file_paths2
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
199 --${additional_reads.singlePaired.type_paired}-12 $library '${read}'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
200 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
201 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
202 #else
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
203 #for $read in $fw_reads2
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
204 --${additional_reads.singlePaired.type_paired}-1 $library '${read}'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
205 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
206 #for $read in $rv_reads2
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
207 --${additional_reads.singlePaired.type_paired}-2 $library '${read}'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
208 --${additional_reads.singlePaired.type_paired}-or $library $additional_reads.singlePaired.orientation
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
209 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
210 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
211 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
212
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
213 <token name="@PIPELINE_OPTIONS@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
214 #for $i in $mode_sel
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
215 $i
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
216 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
217 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
218
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
219 <token name="@KMER@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
220 #if $kmer_cond.kmer_sel != 'auto'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
221 -k '$kmer_cond.manual'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
222 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
223 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
224
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
225 <token name="@PHREDOFFSET@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
226 #if $phred_offset != 'auto'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
227 --phred-offset $phred_offset
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
228 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
229 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
230
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
231 <!-- ADDITIONAL INPUTS-->
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
232
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
233 <token name="@PREPROCESS_CONTIGS_FILES@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
234 #if $arf.trusted_contigs
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
235 mkdir -p trusted_contigs &&
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
236 #set trusted_contigs = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
237 #for $i, $input_file in enumerate($arf.trusted_contigs,1)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
238 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
239 #set $fname = 'file' + str($i) + '.' + $ext
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
240 #set $file_path = 'trusted_contigs/' + $fname
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
241 ln -s '$input_file' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
242 $trusted_contigs.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
243 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
244 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
245 #if $arf.untrusted_contigs
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
246 mkdir -p untrusted_contigs &&
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
247 #set untrusted_contigs = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
248 #for $i, $input_file in enumerate($arf.untrusted_contigs,1)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
249 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
250 #set $fname = 'file' + str($i) + '.' + $ext
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
251 #set $file_path = 'untrusted_contigs/' + $fname
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
252 ln -s '$input_file' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
253 $untrusted_contigs.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
254 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
255 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
256 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
257
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
258 <token name="@PREPROCESS_NANOPORE_PACBIO_FILES@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
259 #if $arf.nanopore
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
260 mkdir -p nanopore_reads &&
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
261 #set nanopore_reads = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
262 #for $i, $input_file in enumerate($arf.nanopore,1)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
263 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
264 #set $fname = 'file' + str($i) + '.' + $ext
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
265 #set $file_path = 'nanopore_reads/' + $fname
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
266 ln -s '$input_file' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
267 $nanopore_reads.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
268 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
269 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
270 #if $arf.pacbio
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
271 mkdir -p pacbio_reads &&
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
272 #set pacbio_reads = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
273 #for $i, $input_file in enumerate($arf.pacbio,1)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
274 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
275 #set $fname = 'file' + str($i) + '.' + $ext
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
276 #set $file_path = 'pacbio_reads/' + $fname
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
277 ln -s '$input_file' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
278 $pacbio_reads.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
279 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
280 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
281 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
282
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
283 <token name="@PREPROCESS_SANGER_FILES@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
284 #if $arf.sanger
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
285 mkdir -p sanger_reads &&
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
286 #set sanger_reads = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
287 #for $i, $input_file in enumerate($arf.sanger,1)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
288 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
289 #set $fname = 'file' + str($i) + '.' + $ext
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
290 #set $file_path = 'sanger_reads/' + $fname
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
291 ln -s '$input_file' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
292 $sanger_reads.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
293 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
294 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
295 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
296
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
297 <token name="@PREPROCESS_FL_RNA_FILES@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
298 #if $arf.flrna
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
299 mkdir -p flrna_reads &&
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
300 #set flrna_reads = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
301 #for $i, $input_file in enumerate($arf.flrna,1)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
302 #set $ext = $input_file.ext.replace('fastqsanger', 'fastq')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
303 #set $fname = 'file' + str($i) + '.' + $ext
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
304 #set $file_path = 'flrna_reads/' + $fname
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
305 ln -s '$input_file' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
306 $flrna_reads.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
307 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
308 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
309 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
310
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
311 <token name="@PREPROCESS_ASSEMBLY_GRAPH_FILES@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
312 #if $arf.assembly_graph
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
313 mkdir -p assembly_graphs &&
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
314 #set assembly_graphs = []
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
315 #for $i, $input_file in enumerate($arf.assembly_graph,1)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
316 #set $ext = $input_file.ext.replace('gfa1', 'gfa')
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
317 #set $fname = 'file' + str($i) + '.' + $ext
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
318 #set $file_path = 'assembly_graphs/' + $fname
1
11d7955eddf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 370cc20429f3b9e68792b71865b05165cac3ad77"
iuc
parents: 0
diff changeset
319 ln -s '$input_file' '$file_path' &&
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
320 $assembly_graphs.append($file_path)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
321 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
322 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
323 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
324
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
325
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
326 <token name="@NANOPORE_PACBIO@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
327 #if $arf.nanopore
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
328 #for $read in $nanopore_reads
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
329 --nanopore $read
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
330 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
331 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
332 #if $arf.pacbio
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
333 #for $read in $pacbio_reads
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
334 --pacbio $read
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
335 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
336 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
337 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
338
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
339
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
340 <token name="@SANGER@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
341 #if $arf.sanger
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
342 #for $read in $sanger_reads
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
343 --sanger $read
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
344 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
345 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
346 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
347
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
348 <token name="@FL_RNA@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
349 #if $arf.flrna
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
350 #for $read in $flrna_reads
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
351 --fl-rna $read
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
352 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
353 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
354 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
355
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
356 <token name="@ASSEMBLY_GRAPH@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
357 #if $arf.assembly_graph
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
358 #for $graph in $assembly_graphs
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
359 --assembly-graph $graph
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
360 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
361 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
362 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
363
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
364 <token name="@CONTIGS@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
365 #if $arf.trusted_contigs
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
366 #for $read in $trusted_contigs
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
367 --trusted-contigs $read
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
368 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
369 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
370 #if $arf.untrusted_contigs
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
371 #for $read in $untrusted_contigs
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
372 --untrusted-contigs $read
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
373 #end for
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
374 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
375 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
376
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
377 <token name="@LIBRARY_NUMBER@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
378 #if $additional_reads.selector == 'true' and $additional_reads.library_number == 'false'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
379 #set $library += 1
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
380 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
381 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
382
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
383 <!-- POSTPROCESSING -->
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
384
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
385 <token name="@STATS@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
386 #if 'cs' in $optional_output
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
387 && test -f 'output/contigs.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/contigs.fasta' > '$out_cs' || echo 'No contigs.fasta.'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
388 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
389 #if 'ss' in $optional_output
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
390 && test -f 'output/scaffolds.fasta' && python '$__tool_directory__/write_tsv_script.py' < 'output/scaffolds.fasta' > '$out_ss' || echo 'No scaffolds.fasta.'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
391 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
392 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
393
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
394 <token name="@CORRECTED@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
395 #if 'corrected' in $optional_output
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
396 && test -d 'output/corrected' && zip -q -r 'corrected.zip' 'output/corrected/*.fastq.gz' || echo 'No output files for corrected reads.'
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
397 #end if
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
398 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
399
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
400 <!--
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
401 input
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
402 -->
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
403
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
404 <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.">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
405 <conditional name="singlePaired">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
406 <param name="sPaired" type="select" label="Single-end or paired-end short-reads" help="@HELP@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
407 <option value="single" selected="true">Single-end</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
408 <option value="paired">Paired-end: individual datasets</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
409 <option value="paired_interlaced">Paired-end: interlaced reads</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
410 <option value="paired_collection">Paired-end: list of dataset pairs</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
411 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
412 <when value="single">
5df83f4bad67 "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@"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
414 </when>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
415 <when value="paired">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
416 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: forward reads"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
417 <param format="@FORMAT@" name="input2" type="data" multiple="true" label="@LABEL@: reverse reads"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
418 <expand macro="type_paired"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
419 <expand macro="orientation"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
420 </when>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
421 <when value="paired_interlaced">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
422 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
423 <expand macro="type_paired"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
424 <expand macro="orientation"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
425 </when>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
426 <when value="paired_collection">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
427 <param format="@FORMAT@" name="input" type="data_collection" collection_type="list:paired" label="@LABEL@: collection"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
428 <expand macro="type_paired"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
429 <expand macro="orientation"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
430 </when>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
431 </conditional>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
432 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
433
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
434 <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.">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
435 <conditional name="singlePaired">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
436 <param name="sPaired" type="select" label="Pair-end reads input format" help="@HELP@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
437 <option value="paired" selected="true">Paired-end: individual datasets</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
438 <option value="paired_interlaced">Paired-end: interlaced reads</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
439 <option value="paired_collection">Paired-end: list of dataset pairs</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
440 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
441 <when value="paired">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
442 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: forward reads"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
443 <param format="@FORMAT@" name="input2" type="data" multiple="true" label="@LABEL@: reverse reads"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
444 <expand macro="type_paired"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
445 <expand macro="orientation"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
446 </when>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
447 <when value="paired_interlaced">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
448 <param format="@FORMAT@" name="input1" type="data" multiple="true" label="@LABEL@: interlaced"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
449 <expand macro="type_paired"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
450 <expand macro="orientation"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
451 </when>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
452 <when value="paired_collection">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
453 <param format="@FORMAT@" name="input" type="data_collection" collection_type="list:paired" label="@LABEL@: collection"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
454 <expand macro="type_paired"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
455 <expand macro="orientation"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
456 </when>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
457 </conditional>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
458 <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.">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
459 <option value="true" selected="true">True</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
460 <option value="false">False</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
461 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
462 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
463
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
464 <xml name="orientation">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
465 <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.">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
466 <option value="fr" selected="true"><![CDATA[FR (-> <-)]]></option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
467 <option value="rf"><![CDATA[RF (<- ->)]]></option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
468 <option value="ff"><![CDATA[FF (-> ->)]]></option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
469 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
470 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
471
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
472 <xml name="type_paired">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
473 <param name="type_paired" type="select" label="Type of paired-reads"
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
474 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,
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
475 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.">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
476 <option value="pe" selected="true">Default (--pe)</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
477 <option value="mp">Mate-pair reads (--mp)</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
478 <option value="hqmp">High-quality Nextera mate-pair reads (--hqmp)</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
479 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
480 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
481
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
482 <xml name="input_additional_files_all" token_format="" token_label="" token_help="">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
483 <conditional name="additional_reads">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
484 <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).">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
485 <option value="false" selected="true">Disabled</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
486 <option value="true">Enabled</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
487 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
488 <when value="true">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
489 <expand macro="input_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)" help="@HELP@"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
490 <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.">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
491 <option value="true" selected="true">True</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
492 <option value="false">False</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
493 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
494 </when>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
495 <when value="false"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
496 </conditional>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
497 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
498
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
499 <xml name="input_additional_files_paired" token_format="" token_label="" token_help="" >
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
500 <conditional name="additional_reads">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
501 <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).">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
502 <option value="false" selected="true">Disabled</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
503 <option value="true">Enabled</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
504 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
505 <when value="true">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
506 <expand macro="input_files_paired" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTA/FASTQ file(s)" help="@HELP@"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
507 </when>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
508 <when value="false"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
509 </conditional>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
510 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
511
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
512 <xml name="covcutoff">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
513 <conditional name="cov_cond">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
514 <param argument="--cov-cutoff" type="select" label="Set coverage cutoff option" help="When set to 'auto' SPAdes automatically computes coverage threshold using conservative strategy">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
515 <option value="off">Off</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
516 <option value="auto">Auto</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
517 <option value="value">User specific</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
518 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
519 <when value="off"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
520 <when value="auto"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
521 <when value="value">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
522 <param name="manual" type="float" min="0" value="" label="Set value"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
523 </when>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
524 </conditional>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
525 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
526 <xml name="pipeline_options">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
527 <param name="mode_sel" type="select" label="Pipeline options" multiple="true" optional="true" display="checkboxes" help="Error correction requires FASTQ input files.">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
528 <option value="--disable-rr">Disable repeat resolution (--disable-rr)</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
529 <yield/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
530 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
531 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
532 <xml name="kmer" token_help="" token_default="21,33,55,77">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
533 <conditional name="kmer_cond">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
534 <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.">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
535 <option value="auto">Auto</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
536 <option value="manual">User specific</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
537 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
538 <when value="auto"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
539 <when value="manual">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
540 <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)">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
541 <sanitizer invalid_char="">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
542 <valid initial="string.digits">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
543 <add value="," />
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
544 </valid>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
545 </sanitizer>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
546 <validator type="regex">[0-9,]+</validator>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
547 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
548 </when>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
549 </conditional>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
550 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
551 <xml name="nanopore_pacbio">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
552 <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"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
553 <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"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
554 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
555 <xml name="flrna">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
556 <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."/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
557 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
558
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
559 <xml name="phred">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
560 <param argument="--phred-offset" type="select" label="Set Phred quality offset" help="Phred quality offset in the input reads. Default: auto-detect">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
561 <option value="auto" selected="true">Auto</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
562 <option value="33">33 (Sanger)</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
563 <option value="64">64 (Illumina)</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
564 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
565 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
566 <xml name="reads" token_paramname="reads" token_help="" token_label="">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
567 <param name="@PARAMNAME@" type="data" format="fastq,fastq.gz" label="@LABEL@ reads" help="@HELP@"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
568 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
569 <xml name="sanger">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
570 <param argument="--sanger" type="data" format="fastq,fastq.gz" multiple="true" optional="true" label="Sanger reads"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
571 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
572 <xml name="contigs">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
573 <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."/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
574 <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."/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
575 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
576 <xml name="assembly_graph">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
577 <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."/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
578 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
579 <xml name="optional_output">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
580 <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.">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
581 <option value="ag" selected="true">Assembly graph</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
582 <option value="ags" selected="true">Assembly graph with scaffolds</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
583 <option value="cn" selected="true">Contigs</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
584 <option value="cp">Contigs paths</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
585 <option value="cr">Corrected reads</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
586 <option value="cs">Contigs stats</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
587 <option value="l">Log</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
588 <option value="sc" selected="true">Scaffolds</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
589 <option value="sp">Scaffolds paths</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
590 <option value="ss">Scaffolds stats</option>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
591 </param>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
592 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
593 <!--
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
594 output
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
595 -->
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
596
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
597 <xml name="out_ag">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
598 <data name="out_ag" format="fastg" from_work_dir="output/assembly_graph.fastg" label="${tool.name} on ${on_string}: Assembly graph">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
599 <filter>'ag' in optional_output</filter>
7
d5fb354f745d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 6
diff changeset
600 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
601 </data>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
602 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
603 <xml name="out_ags">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
604 <data name="out_ags" format="txt" from_work_dir="output/assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: Assembly graph with scaffolds">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
605 <filter>'ags' in optional_output</filter>
7
d5fb354f745d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 6
diff changeset
606 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
607 </data>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
608 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
609 <xml name="out_cn">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
610 <data name="out_cn" format="fasta" from_work_dir="output/contigs.fasta" label="${tool.name} on ${on_string}: Contigs">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
611 <filter>'cn' in optional_output</filter>
7
d5fb354f745d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 6
diff changeset
612 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
613 </data>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
614 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
615 <xml name="out_cp">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
616 <data name="out_cp" format="txt" from_work_dir="output/contigs.paths" label="${tool.name} on ${on_string}: Contigs paths">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
617 <filter>'cp' in optional_output</filter>
7
d5fb354f745d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 6
diff changeset
618 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
619 </data>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
620 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
621 <xml name="out_cr">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
622 <!-- some mode combinations create fastq, some fasta -->
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
623 <collection name="out_cr" type="list" label="${tool.name} on ${on_string}: Corrected reads">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
624 <filter>'cr' in optional_output</filter>
7
d5fb354f745d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 6
diff changeset
625 <filter>'operation_mode' not in vars() or operation_mode != '--only-assembler'</filter>
d5fb354f745d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 6
diff changeset
626 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.cor\.fastq\.gz" format="fastq" directory="output/corrected"/>
d5fb354f745d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 6
diff changeset
627 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.cor\.fasta\.gz" format="fasta" directory="output/corrected"/>
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
628 </collection>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
629 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
630 <xml name="out_cs">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
631 <data name="out_cs" format="tabular" label="${tool.name} on ${on_string}: Contigs stats">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
632 <actions>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
633 <action name="column_names" type="metadata" default="name,length,coverage"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
634 </actions>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
635 <filter>'cs' in optional_output</filter>
7
d5fb354f745d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 6
diff changeset
636 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
637 </data>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
638 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
639 <xml name="out_l">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
640 <data name="out_l" format="txt" from_work_dir="output/spades.log" label="${tool.name} on ${on_string}: Log">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
641 <filter>'l' in optional_output</filter>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
642 </data>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
643 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
644 <xml name="out_sc">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
645 <data name="out_sc" format="fasta" from_work_dir="output/scaffolds.fasta" label="${tool.name} on ${on_string}: Scaffolds">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
646 <filter>'sc' in optional_output</filter>
7
d5fb354f745d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 6
diff changeset
647 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
648 </data>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
649 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
650 <xml name="out_sp">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
651 <data name="out_sp" format="txt" from_work_dir="output/scaffolds.paths" label="${tool.name} on ${on_string}: Scaffolds paths">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
652 <filter>'sp' in optional_output</filter>
7
d5fb354f745d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 6
diff changeset
653 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
654 </data>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
655 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
656 <xml name="out_ss">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
657 <data name="out_ss" format="tabular" label="${tool.name} on ${on_string}: Scaffolds stats">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
658 <actions>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
659 <action name="column_names" type="metadata" default="name,length,coverage"/>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
660 </actions>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
661 <filter>'ss' in optional_output</filter>
7
d5fb354f745d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
iuc
parents: 6
diff changeset
662 <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter>
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
663 </data>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
664 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
665 <xml name="out_rs">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
666 <data name="out_rs" format="fasta" from_work_dir="output/raw_scaffolds.fasta" label="${tool.name} on ${on_string}: Raw scaffolds">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
667 <filter>'rs' in optional_output</filter>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
668 </data>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
669 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
670 <xml name="out_b">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
671 <data name="out_b" format="txt" from_work_dir="output/hmm_statistics.txt" label="${tool.name} on ${on_string}: HMM statistics">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
672 <filter>'b' in optional_output</filter>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
673 </data>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
674 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
675 <xml name="out_dg">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
676 <data name="out_dg" format="fasta" from_work_dir="output/domain_graph.dot" label="${tool.name} on ${on_string}: Domain graph">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
677 <filter>'dg' in optional_output</filter>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
678 </data>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
679 </xml>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
680 <!--
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
681 help
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
682 -->
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
683
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
684 <token name="@HELP_IN@"><![CDATA[
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
685
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
686 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.
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
687
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
688 To run SPAdes 3.15.3 you need at least one library of the following types:
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
689
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
690 - Illumina paired-end/high-quality mate-pairs/unpaired reads
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
691 - IonTorrent paired-end/high-quality mate-pairs/unpaired reads
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
692 - PacBio CCS reads
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
693 - 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.
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
694
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
695 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.
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
696
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
697 Notes:
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
698
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
699 - It is strongly suggested to provide multiple paired-end and mate-pair libraries according to their insert size (from smallest to longest).
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
700 - It is not recommended to run SPAdes on PacBio reads with low coverage (less than 5).
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
701 - We suggest not to run SPAdes on PacBio reads for large genomes.
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
702 - SPAdes accepts gzip-compressed files.
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
703
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
704 A detailed description can be found in the `input section <https://github.com/ablab/spades/#sec3.1>`_ of the manual.
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
705 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
706 <token name="@HELP_OUT_AG@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
707 - Assembly graph
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
708 </token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
709 <token name="@HELP_OUT_AGS@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
710 - Assembly graph with scaffolds
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
711 </token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
712 <token name="@HELP_OUT_C@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
713 - Contigs
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
714 </token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
715 <token name="@HELP_OUT_CP@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
716 - Contigs paths in the assembly graph
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
717 </token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
718 <token name="@HELP_OUT_CS@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
719 - Contigs stats
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
720 </token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
721 <token name="@HELP_OUT_CR@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
722 - Corrected reads by BayesHammer
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
723 </token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
724 <token name="@HELP_OUT_L@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
725 - Log file
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
726 </token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
727 <token name="@HELP_OUT_S@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
728 - Scaffolds (recommended for use as resulting sequences)
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
729 </token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
730 <token name="@HELP_OUT_SP@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
731 - Scaffolds paths in the assembly graph
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
732 </token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
733 <token name="@HELP_OUT_SS@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
734 - Scaffolds stats
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
735 </token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
736 <token name="@HELP_WID@">
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
737 SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
738 </token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
739 <token name="@IONTORRENT@"><![CDATA[
6
48cf45a53456 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 35f71aa486d8754ee6a8387659032fc7c93d1be3
iuc
parents: 5
diff changeset
740 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://github.com/ablab/spades#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.
0
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
741
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
742 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.
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
743
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
744 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.
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
745
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
746 ]]></token>
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
747
5df83f4bad67 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 8734db131db6f76697b500b30f18ee7723d61813"
iuc
parents:
diff changeset
748 </macros>