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annotate abyss-pe.xml @ 12:a929ce596a34 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit c083399ddb31b026aaab1d600d8789bf56cf4d4b
author iuc
date Mon, 18 Sep 2023 11:05:22 +0000
parents 7547fcab5d19
children 0124fce4654a
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10
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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1 <tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
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2 <description>de novo sequence assembler</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.3.6</token>
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a929ce596a34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit c083399ddb31b026aaab1d600d8789bf56cf4d4b
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5 <token name="@VERSION_SUFFIX@">1</token>
0
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6 <xml name="reads_conditional">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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7 <conditional name="reads">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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8 <param name="reads_selector" type="select" label="Type of paired-end datasets">
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9 <option value="paired">2 separate datasets</option>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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10 <option value="paired_collection">1 paired dataset collection</option>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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11 <option value="paired_il">1 dataset of interleaved reads</option>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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12 </param>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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13 <when value="paired">
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14 <param name="reads1" type="data" format="fasta,fastq,fastq.gz" label="Paired-end reads 1" />
fa5259cc561b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
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15 <param name="reads2" type="data" format="fasta,fastq,fastq.gz" label="Paired-end reads 2" />
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16 </when>
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17 <when value="paired_collection">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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18 <param name="reads_coll" type="data_collection" collection_type="paired" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads collection" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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19 </when>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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20 <when value="paired_il">
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21 <param name="reads_il" type="data" format="fasta,fastq,fastq.gz" label="Interleaved paired-end reads" />
0
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22 </when>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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23 </conditional>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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24 </xml>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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25 </macros>
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26 <xrefs>
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27 <xref type="bio.tools">abyss</xref>
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28 </xrefs>
0
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29 <requirements>
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30 <requirement type="package" version="@TOOL_VERSION@">abyss</requirement>
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31 <requirement type="package" version="0.7.17">bwa</requirement>
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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32 </requirements>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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33 <stdio>
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34 <!-- Anything other than zero is an error -->
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35 <exit_code range="1:" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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36 <!-- In case the return code has not been set propery check stderr too -->
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37 <regex match="Error:" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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38 <regex match="Exception:" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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39 </stdio>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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40 <version_command>ABYSS --version | head -n 1</version_command>
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41 <command><![CDATA[
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42
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43 #def get_link_fname($data, $prefix, $index)
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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44 ## Make a name for symlinked files including extension
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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45 #return ''.join([str($prefix), '_', str($index), '.', str($data.ext)])
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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46 #end def
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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47
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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48 ## Go through all inputs and create symbolic links
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49 #for $i, $v in enumerate($lib_repeat)
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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50 #if $v.reads.reads_selector == 'paired'
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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51 ln -s $v.reads.reads1 $get_link_fname($v.reads.reads1, 'lib_reads1', $i) &&
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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52 ln -s $v.reads.reads2 $get_link_fname($v.reads.reads2, 'lib_reads2', $i) &&
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53 #elif $v.reads.reads_selector == 'paired_collection'
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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54 ln -s $v.reads.reads_coll.forward $get_link_fname($v.reads.reads_coll.forward, 'lib_reads_coll_forward', $i) &&
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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55 ln -s $v.reads.reads_coll.reverse $get_link_fname($v.reads.reads_coll.reverse, 'lib_reads_coll_reverse', $i) &&
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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56 #else
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57 ln -s $v.reads.reads_il $get_link_fname($v.reads.reads_il, 'lib_reads_il', $i) &&
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58 #end if
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59 #end for
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60
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61 #for $i, $v in enumerate($mp_repeat)
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62 #if $v.reads.reads_selector == 'paired'
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63 ln -s $v.reads.reads1 $get_link_fname($v.reads.reads1, 'mp_reads1', $i) &&
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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64 ln -s $v.reads.reads2 $get_link_fname($v.reads.reads2, 'mp_reads2', $i) &&
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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65 #elif $v.reads.reads_selector == 'paired_collection'
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66 ln -s $v.reads.reads_coll.forward $get_link_fname($v.reads.reads_coll.forward, 'mp_reads_coll_forward', $i) &&
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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67 ln -s $v.reads.reads_coll.reverse $get_link_fname($v.reads.reads_coll.reverse, 'mp_reads_coll_reverse', $i) &&
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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68 #else
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69 ln -s $v.reads.reads_il $get_link_fname($v.reads.reads_il, 'mp_reads_il', $i) &&
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
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70 #end if
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71 #end for
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72
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73 #if str($se_reads) != 'None'
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74 #for $i, $v in enumerate($se_reads)
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75 ln -s $v $get_link_fname($v, 'se_reads', $i) &&
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76 #end for
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77 #end if
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78
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79 #if str($long_seqs) != 'None'
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80 #for $i, $v in enumerate($long_seqs)
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81 ln -s $v $get_link_fname($v, 'long_seqs', $i) &&
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82 #end for
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diff changeset
83 #end if
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
iuc
parents: 9
diff changeset
84
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
85 abyss-pe
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
86 name=abyss
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
87 j=\${GALAXY_SLOTS:-1}
12
a929ce596a34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit c083399ddb31b026aaab1d600d8789bf56cf4d4b
iuc
parents: 11
diff changeset
88 B=\$((\${GALAXY_MEMORY_MB:-2048} * 9 /10 ))M
a929ce596a34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit c083399ddb31b026aaab1d600d8789bf56cf4d4b
iuc
parents: 11
diff changeset
89
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
90 k=$k
1
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
91
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
92 #if str($K)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
93 K=$K
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
94 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
95 #if str($q)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
96 q=$q
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
97 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
98 #if str($Q)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
99 Q=$Q
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
100 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
101 #if str($e)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
102 e=$e
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
103 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
104 #if str($E)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
105 E=$E
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
106 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
107 #if str($t)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
108 t=$t
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
109 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
110 #if str($c)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
111 c=$c
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
112 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
113 #if str($b)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
114 b=$b
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
115 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
116 #if $SS
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
117 SS=--SS
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
118 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
119 #if str($m)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
120 m=$m
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
121 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
122 #if str($p)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
123 p=$p
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
124 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
125 #if str($a)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
126 a=$a
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
127 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
128 #if str($l)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
129 l=$l
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
130 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
131 #if str($s)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
132 s=$s
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
133 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
134 #if str($n)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
135 n=$n
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
136 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
137 #if str($d)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
138 d=$d
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
139 #end if
7
841084c5fc46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit e14b8554ee2a7d00b98c7cb863a07245d29ab93f"
iuc
parents: 6
diff changeset
140 #if $S
841084c5fc46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit e14b8554ee2a7d00b98c7cb863a07245d29ab93f"
iuc
parents: 6
diff changeset
141 S='$S'
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
142 #end if
7
841084c5fc46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit e14b8554ee2a7d00b98c7cb863a07245d29ab93f"
iuc
parents: 6
diff changeset
143 #if $N
841084c5fc46 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit e14b8554ee2a7d00b98c7cb863a07245d29ab93f"
iuc
parents: 6
diff changeset
144 N='$N'
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
145 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
146 #if $lib_repeat
10
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
iuc
parents: 9
diff changeset
147 lib='${' '.join(['lib'+str($i) for $i in range(len($lib_repeat))])}'
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
148 #for $i, $v in enumerate($lib_repeat)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
149 #if $v.reads.reads_selector == 'paired'
10
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
iuc
parents: 9
diff changeset
150 lib${i}='${get_link_fname($v.reads.reads1, "lib_reads1", $i)} ${get_link_fname($v.reads.reads2, "lib_reads2", $i)}'
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
151 #elif $v.reads.reads_selector == 'paired_collection'
10
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
iuc
parents: 9
diff changeset
152 lib${i}='$get_link_fname($v.reads.reads_coll.forward, "lib_reads_coll_forward", $i)} ${get_link_fname($v.reads.reads_coll.reverse, "lib_reads_coll_reverse", $i)}'
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
153 #else
10
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
iuc
parents: 9
diff changeset
154 lib${i}='${get_link_fname($v.reads.reads_il, "lib_reads_il", $i)}'
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
155 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
156 #end for
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
157 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
158 #if str($se_reads) != 'None'
10
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
iuc
parents: 9
diff changeset
159 se='${' '.join([$get_link_fname($v, "se_reads", $i) for $i, $v in enumerate($se_reads)])}'
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
160 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
161 #if $mp_repeat
10
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
iuc
parents: 9
diff changeset
162 mp='${' '.join(['mp'+str($i) for $i in range(len($mp_repeat))])}'
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
163 #for $i, $v in enumerate($mp_repeat)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
164 #if $v.reads.reads_selector == 'paired'
10
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
iuc
parents: 9
diff changeset
165 mp${i}='${get_link_fname($v.reads.reads1, "mp_reads1", $i)} ${get_link_fname($v.reads.reads2, "mp_reads2", $i)}'
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
166 #elif $v.reads.reads_selector == 'paired_collection'
10
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
iuc
parents: 9
diff changeset
167 mp${i}='$get_link_fname($v.reads.reads_coll.forward, "mp_reads_coll_forward", $i)} ${get_link_fname($v.reads.reads_coll.reverse, "mp_reads_coll_reverse", $i)}'
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
168 #else
10
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
iuc
parents: 9
diff changeset
169 mp${i}='${get_link_fname($v.reads.reads_il, "mp_reads_il", $i)}'
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
170 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
171 #end for
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
172 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
173 #if str($long_seqs) != 'None'
10
8f1b150a2487 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 4ad8aac500f821c9ad069e5e8723a0d8af4d2700"
iuc
parents: 9
diff changeset
174 long='${' '.join(['long'+str($i) for $i in range(len($long_seqs))])}'
2
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175 #for $i, $v in enumerate($long_seqs)
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176 long$i='${get_link_fname($v, "long_seqs", $i)}'
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177 #end for
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178 #end if
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179 ]]></command>
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180
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181 <inputs>
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182 <repeat name="lib_repeat" title="Paired-end library" help="(lib)">
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183 <expand macro="reads_conditional" />
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184 </repeat>
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185 <param name="se_reads" argument="se" type="data" multiple="true" optional="true" format="fasta,fastq,fastq.gz" label="Single-end reads" />
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186 <repeat name="mp_repeat" title="Mate-pair library" help="The mate-pair libraries are used only for scaffolding and do not contribute towards the consensus sequence (mp)">
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187 <expand macro="reads_conditional" />
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188 </repeat>
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189 <param name="long_seqs" argument="long" type="data" multiple="true" optional="true" format="fasta,fastq,fastq.gz" label="Long sequences" help="Long sequence libraries are used only for rescaffolding and do not contribute towards the consensus sequence" />
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190 <param argument="k" type="integer" value="41" label="K-mer length (in bp)" help="The length of a k-mer (when -K is not set) or the span of a k-mer pair (when K is set)" />
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191 <param argument="K" type="integer" value="" optional="true" label="The length (in bp) of a single k-mer in a k-mer pair" help="Optional" />
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192 <param argument="q" type="integer" value="3" max="40" optional="true" label="Minimum base quality when trimming" help="Trim bases from the ends of reads whose quality is less than this value" />
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193 <param argument="Q" type="integer" value="0" max="40" optional="true" label="Minimum base quality" help="Mask all bases of reads whose quality is less than this value as 'N'" />
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194 <param argument="e" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage" help="Erode bases at the ends of blunt contigs with coverage less than this value. Defaults to round(sqrt(median))" />
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195 <param argument="E" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage per strand" help="Erode bases at the ends of blunt contigs with coverage less than this value on either strand. Defaults to 1 if sqrt(median) &gt; 2 else 0" />
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196 <param argument="t" type="integer" value="" optional="true" label="Maximum length of blunt contigs to trim" help="Defaults to the value of k" />
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197 <param argument="c" type="float" value="" optional="true" label="Minimum mean k-mer coverage of a unitig" help="Defaults to sqrt(median)" />
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198 <param argument="b" type="integer" value="" optional="true" label="Maximum length of a bubble (in bp)" help="abyss-pe has two bubble popping stages. The default limits are 3*k bp for ABYSS and 10000 bp for PopBubbles" />
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199 <param argument="SS" type="boolean" label="Assemble in strand-specific mode" help="Requires that all libraries are strand-specific RNA-Seq libraries. Assumes that the first read in a read pair is reveresed with respect to the transcripts sequenced" />
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200 <param argument="m" type="integer" value="" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" help="Defaults to 0 (interpreted as k - 1) if mate-pair libraries are provided or if k&lt;=50, otherwise 50" />
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201 <param argument="p" type="float" value="0.9" optional="true" label="Minimum sequence identity of a bubble" />
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202 <param argument="a" type="integer" value="2" min="0" optional="true" label="Maximum number of branches of a bubble" />
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203 <param argument="l" type="integer" value="" min="1" optional="true" label="Minimum alignment length of a read (in bp)" help="Defaults to the value of k" />
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204 <param argument="s" type="integer" value="200" min="0" optional="true" label="Minimum unitig length required for building contigs (in bp)" help="The seed length should be at least twice the value of k. If more sequence is assembled than the expected genome size, try increasing this value" />
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205 <param argument="n" type="integer" value="10" min="0" optional="true" label="Minimum number of pairs required for building contigs" />
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206 <param argument="d" type="integer" value="6" min="0" optional="true" label="Allowable error of a distance estimate (in bp)" />
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207 <param argument="S" type="text" value="" label="Minimum contig size required for building scaffolds (in bp)" help="It can be an interval. Defaults to 100-5000">
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208 <validator type="regex" message="Must be a an integer or an interval">^([0-9]+(-[0-9]+)?)?$</validator>
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209 </param>
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210 <param argument="N" type="text" value="" label="Minimum number of pairs required for building scaffolds" help="It can be an interval. Defaults to 15-20">
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211 <validator type="regex" message="Must be a an integer or an interval">^([0-9]+(-[0-9]+)?)?$</validator>
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212 </param>
0
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213 </inputs>
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214
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215 <outputs>
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216 <data name="unitigs" format="fasta" label="${tool.name} on ${on_string}: unitigs" from_work_dir="abyss-unitigs.fa" />
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217 <data name="contigs_outfile" format="fasta" label="${tool.name} on ${on_string}: contigs" from_work_dir="abyss-contigs.fa">
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218 <filter>lib_repeat</filter>
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219 </data>
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220 <data name="scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-scaffolds.fa">
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221 <filter>lib_repeat or mp_repeat</filter>
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222 </data>
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223 <data name="long_scaffolds" format="fasta" label="${tool.name} on ${on_string}: long scaffolds" from_work_dir="abyss-long-scaffs.fa">
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224 <filter>long_seqs</filter>
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225 </data>
0
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226 <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" />
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227 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" />
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228 </outputs>
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229
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230 <tests>
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231 <test expect_num_outputs="5">
0
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232 <repeat name="lib_repeat">
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233 <conditional name="reads">
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234 <param name="reads_selector" value="paired" />
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235 <param name="reads1" ftype="fastqsanger.gz" value="assembly_sample-R1.fastq.gz" />
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236 <param name="reads2" ftype="fastqsanger.gz" value="assembly_sample-R2.fastq.gz" />
0
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237 </conditional>
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238 </repeat>
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239 <param name="k" value="50" />
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240 <output name="unitigs" file="abyss-unitigs1.fa" />
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241 <output name="contigs_outfile" file="abyss-contigs1.fa" />
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242 <output name="scaffolds" file="abyss-scaffolds1.fa" />
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243 <output name="indels" file="empty_file.fasta" />
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244 <output name="stats" file="abyss-stats1.tab" />
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245 </test>
12
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246 <test expect_num_outputs="3">
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247 <param name="se_reads" ftype="fastq.gz" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
0
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248 <param name="k" value="50" />
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249 <output name="unitigs" file="abyss-unitigs2.fa" />
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250 <output name="indels" file="empty_file.fasta" />
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251 <output name="stats" file="abyss-stats2.tab" />
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252 </test>
12
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253 <test expect_num_outputs="4">
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254 <param name="se_reads" ftype="fasta" value="assembly_sample-R1.fasta,assembly_sample-R2.fasta" />
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255 <param name="long_seqs" ftype="fasta" value="assembly_sample-R2.fasta" />
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256 <param name="k" value="50" />
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257 <output name="unitigs" file="abyss-unitigs3.fa" />
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258 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />
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259 <output name="indels" file="empty_file.fasta" />
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260 <output name="stats" file="abyss-stats3.tab" />
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261 </test>
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262 </tests>
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263 <help><![CDATA[
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264 **What it does**
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265
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266 `ABySS`_ is a de novo sequence assembler intended for short paired-end reads and large genomes.
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267
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268 **Input**
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269
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270 Input files should be FASTA or FASTQ files.
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271
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272 For paired reads, a pair of reads must be named with the suffixes /1 and /2 to identify the first and second read, or the reads may be named identically. The paired reads may be in separate files or interleaved in a single file.
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273
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274 At least a paired-end library or a single-end library must be provided.
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275
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276 Contigs are generated only if at least a paired-end library is provided. Scaffolds are generated only if at least a paired-end library or a mate-pair library is provided.
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277
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278 **Description**
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279
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280 This tool performs the complete ABySS pipeline using abyss-pe, described in https://github.com/bcgsc/abyss/blob/master/doc/flowchart.pdf .
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281
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282 **License and citation**
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283
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284 This Galaxy tool is Copyright © 2015-2021 `Earlham Institute`_ and is released under the `MIT license`_.
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285
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286 .. _Earlham Institute: http://www.earlham.ac.uk/
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287 .. _MIT license: https://opensource.org/licenses/MIT
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288
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289 You can use this tool only if you agree to the license terms of: `ABySS`_.
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290
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291 .. _ABySS: https://github.com/bcgsc/abyss
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292 ]]></help>
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293 <citations>
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294 <citation type="doi">doi:10.1101/gr.214346.116</citation>
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295 <citation type="doi">10.1101/gr.089532.108</citation>
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296 </citations>
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297 </tool>