Mercurial > repos > devteam > velvet

annotate velvetg.xml @ 2:088bf697a4ce draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet commit ccce07eb8b612cbe09702214d3184b0085c055a8"
author iuc
date Sun, 24 Jan 2021 15:39:45 +0000
parents c397035f715d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
diff changeset
1 <tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.2">
0
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 <description>Velvet sequence assembler for very short reads</description>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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3 <macros>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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4 <import>macros.xml</import>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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5 </macros>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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6 <expand macro="requirements"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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7 <expand macro="stdio"/>
1
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
diff changeset
8 <version_command><![CDATA[
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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9 velvetg 2>&1 | grep "Version" | sed -e 's/Version //'
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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10 ]]></version_command>
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
diff changeset
11 <command><![CDATA[
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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12 ln -s '$input.extra_files_path'/Roadmaps &&
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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13 ln -s '$input.extra_files_path'/Sequences &&
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
diff changeset
14 velvetg .
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
diff changeset
15 #if 'amos' in $add_out:
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
diff changeset
16 -amos_file yes
0
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 #end if
1
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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18 #if 'unused' in $add_out:
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
diff changeset
19 -unused_reads yes
0
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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20 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 $read_trkg
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 #if $coverage.cutoff == "auto":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 -cov_cutoff auto
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 #elif $coverage.cutoff == "value":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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25 -cov_cutoff $coverage.cov_cutoff
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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26 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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27 #if $expected.coverage == "auto":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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28 -exp_cov auto
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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29 #elif $expected.coverage == "value":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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30 -exp_cov $expected.exp_cov
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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32 #if $contig_lgth.use_contig_lgth == "yes":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33 -min_contig_lgth $contig_lgth.min_contig_lgth
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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34 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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35 #if $reads.paired == "yes":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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36 #if int($reads.ins_length) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37 -ins_length $reads.ins_length
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
38 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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39 #if $reads.options.advanced == "yes":
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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diff changeset
40 #if int($reads.options.ins_length_sd) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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41 -ins_length_sd $reads.options.ins_length_sd
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
42 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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43 #if int($reads.options.ins_length2) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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44 -ins_length2 $reads.options.ins_length2
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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45 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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46 #if int($reads.options.ins_length2_sd) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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47 -ins_length2_sd $reads.options.ins_length2_sd
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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48 #end if
1
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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49 #if int($reads.options.ins_length3) > 0:
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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50 -ins_length3 $reads.options.ins_length3
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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51 #end if
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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52 #if int($reads.options.ins_length3_sd) > 0:
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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53 -ins_length3_sd $reads.options.ins_length3_sd
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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54 #end if
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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55 #if int($reads.options.ins_length4) > 0:
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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56 -ins_length4 $reads.options.ins_length4
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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57 #end if
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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58 #if int($reads.options.ins_length4_sd) > 0:
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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59 -ins_length4_sd $reads.options.ins_length4_sd
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
iuc
parents: 0
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60 #end if
0
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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61 #if int($reads.options.ins_length_long) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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62 -ins_length_long $reads.options.ins_length_long
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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63 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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64 #if int($reads.options.ins_length_long_sd) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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65 -ins_length_long_sd $reads.options.ins_length_long_sd
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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66 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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67 #if int($reads.options.max_branch_length) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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68 -max_branch_length $reads.options.max_branch_length
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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69 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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70 #if int($reads.options.max_divergence) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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71 -max_divergence $reads.options.max_divergence
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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72 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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73 #if int($reads.options.max_gap_count) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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74 -max_gap_count $reads.options.max_gap_count
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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75 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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76 #if int($reads.options.min_pair_count) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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77 -min_pair_count $reads.options.min_pair_count
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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78 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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79 #if int($reads.options.max_coverage) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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80 -max_coverage $reads.options.max_coverage
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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81 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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82 #if int($reads.options.long_mult_cutoff) > 0:
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
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83 -long_mult_cutoff $reads.options.long_mult_cutoff
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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84 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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85 $reads.options.scaffolding
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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86 #end if
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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87 #end if
1
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88 ]]></command>
0
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89 <inputs>
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90 <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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91 <conditional name="coverage">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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92 <param name="cutoff" type="select" label="Coverage cutoff" help="">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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93 <option value="none">None</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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94 <option value="auto">Automatically Determined</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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95 <option value="value">Specify Cutoff Value</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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96 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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97 <when value="none"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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98 <when value="auto"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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99 <when value="value">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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100 <param name="cov_cutoff" value="10.0" label="Remove nodes with coverage below" type="float" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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101 </when>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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102 </conditional>
1
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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103 <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="Tracking of short read positions in assembly" help="Generates Graph2 dataset" />
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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104 <conditional name="contig_lgth">
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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105 <param name="use_contig_lgth" type="select" label=" Set minimum contig length" help="minimum contig length exported to contigs.fa file (default: hash length * 2).">
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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106 <option value="no">No</option>
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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107 <option value="yes">Yes</option>
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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108 </param>
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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109 <when value="no"/>
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110 <when value="yes">
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111 <param name="min_contig_lgth" value="42" label="minimum contig length" type="integer" help="minimum contig length exported to contigs.fa file (default: hash length * 2)"/>
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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112 </when>
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113 </conditional>
0
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114 <conditional name="expected">
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115 <param name="coverage" type="select" label="Expected Coverage of Unique Regions" help="">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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116 <option value="none">None</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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117 <option value="auto">Automatically Determined</option>
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118 <option value="value">Specify Expected Value</option>
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119 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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120 <when value="none"/>
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121 <when value="auto"/>
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122 <when value="value">
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123 <param name="exp_cov" value="10.0" label="Remove nodes with coverage below" type="float" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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124 </when>
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125 </conditional>
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126
1
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127 <param name="add_out" type="select" multiple="true" optional="true" label="Additional outputs" help="">
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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128 <option value="amos">Generate a AMOS.afg file</option>
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129 <option value="unused">Generate a UnusedReads fasta file</option>
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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130 <option value="lastgraph">Generate velvet LastGraph file</option>
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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131 </param>
0
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132
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133 <conditional name="reads">
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134 <param name="paired" type="select" label="Using Paired Reads">
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135 <option value="no">No</option>
1
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136 <option value="yes">Yes</option>
0
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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137 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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138 <when value="no"/>
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139 <when value="yes">
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140 <param name="ins_length" value="-1" label="Insert Length in Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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141 <conditional name="options">
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142 <param name="advanced" type="select" label="Velvet Advanced Options">
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143 <option value="no">Use Defaults</option>
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144 <option value="yes">Set Advanced Option Values</option>
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145 </param>
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146 <when value="no"/>
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147 <when value="yes">
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148 <param name="ins_length_sd" value="-1" label="Estimate of Standard Deviation of Paired-End Read dataset(ignored when -1)" type="integer" help="Estimate of standard deviation of Paired-End Read dataset (default: 10% of corresponding length)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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149 <param name="ins_length2" value="-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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150 <param name="ins_length2_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/>
1
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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151 <param name="ins_length3" value="-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/>
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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152 <param name="ins_length3_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/>
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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153 <param name="ins_length4" value="-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/>
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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154 <param name="ins_length4_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/>
0
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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155 <param name="ins_length_long" value="-1" label="Insert Length in Long Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two long paired-end reads"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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156 <param name="ins_length_long_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of Long Paired-End Read dataset (default: 10% of corresponding length)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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157 <param name="max_branch_length" value="-1" label="Maximum branch length (ignored when -1)" type="integer" help="maximum length in base pair of bubble (default: 100)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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158 <param name="max_divergence" value="-1." label="Maximum max_divergence (between .0 and 1., ignored when -1.)" type="float" help="maximum divergence rate between two branches in a bubble (default: .2)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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159 <param name="max_gap_count" value="-1" label="Maximum gap count (ignored when -1)" type="integer" help="maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)"/>
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160 <param name="min_pair_count" value="-1" label="Minimum read-pair count (ignored when -1)" type="integer" help="minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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161 <param name="max_coverage" value="-1." label="Maximum coverage exclusion(ignored when -1.)" type="float" help="Exclude data that has coverage more than this maximum coverage value"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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162 <param name="long_mult_cutoff" value="-1" label="Minimum number of long reads required to merge contigs (ignored when -1)" type="integer" help="minimum number of long reads required to merge contigs (default: 2)"/>
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163 <param name="scaffolding" type="boolean" checked="true" truevalue="-scaffolding yes" falsevalue="-scaffolding no" label="Use Scaffolding" help="Scaffold contigs that it cannot quite be connected (This results in sequences of Ns in the contigs)"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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164 </when>
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165 </conditional>
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166 </when>
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167 </conditional>
1
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168 <!-- TODO
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169 -coverage_mask
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170 -paired_exp_fraction
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171 -alignments
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172 -exportFiltered
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173 -clean
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174 -very_clean
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175 -shortMatePaired-->
0
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176 </inputs>
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177 <outputs>
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178 <data format="txt" name="Graph2" label="${tool.name} on ${on_string}: Graph2" from_work_dir="Graph2">
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179 <filter>read_trkg is True</filter>
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180 </data>
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181 <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph" from_work_dir="LastGraph">
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182 <filter>'lastgraph' in add_out</filter>
0
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183 </data>
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184 <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg" from_work_dir="velvet_asm.afg">
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185 <filter>'amos' in add_out</filter>
0
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186 </data>
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187 <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads" from_work_dir="UnusedReads.fa">
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188 <filter>'unused' in add_out</filter>
0
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189 </data>
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190 <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats" from_work_dir="stats.txt" />
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191 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="contigs.fa" />
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192 </outputs>
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193 <tests>
1
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194 <test expect_num_outputs="5">
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195 <param name="input" value="velvetg_paired.out" ftype="velvet" >
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196 <composite_data value='velvetg_paired/Sequences'/>
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197 <composite_data value='velvetg_paired/Roadmaps'/>
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198 <composite_data value='velvetg_paired/Log'/>
0
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199 </param>
1
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200 <param name="add_out" value="amos,unused,lastgraph" />
0
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201 <param name="read_trkg" value="-read_trkg no" />
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202 <param name="cutoff" value="auto" />
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203 <param name="coverage" value="auto" />
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204 <param name="use_contig_lgth" value="no" />
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205 <param name="paired" value="no" />
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206 <output name="velvet_asm" file="velvetg_paired/velvet_asm.afg" compare="diff"/>
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207 <output name="unused_reads_fasta" file="velvetg_paired/UnusedReads.fa" compare="diff"/>
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208 <output name="LastGraph" file="velvetg_paired/lastgraph.txt" compare="diff"/>
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209 <output name="stats" file="velvetg_paired/stats.txt" compare="diff"/>
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210 <output name="contigs" file="velvetg_paired/contigs.fa" compare="diff"/>
0
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211 </test>
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212 </tests>
1
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213 <help><![CDATA[
0
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214 **What it does**
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215
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216 Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
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217
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218 Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
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219
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220 Read the Velvet `documentation`__ for details on using the Velvet Assembler.
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221
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222 .. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/
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223
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224 .. __: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
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225
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226 ------
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227
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228 **Input formats**
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229
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230 Velvet can input sequence files in the following formats: fasta fastq fasta.gz fastq.gz eland gerald
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231
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232 The input files are prepared for the velvet assembler using **velveth**.
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233
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234 ------
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235
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236 **Outputs**
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237
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238 **Contigs**
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239
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240 The *contigs.fa* file.
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241 This fasta file contains the sequences of the contigs longer than 2k, where k is the word-length used in velveth. If you have specified a min contig length threshold, then the contigs shorter than that value are omitted.
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242 Note that the length and coverage information provided in the header of each contig should therefore be understood in k-mers and in k-mer coverage (cf. 5.1) respectively.
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243 The N's in the sequence correspond to gaps between scaffolded contigs. The number of N's corresponds to the estimated length of the gap. For reasons of compatibility with the archives, any gap shorter than 10bp is represented by a sequence of 10 N's.
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244
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245 **Stats**
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246
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247 The *stats.txt* file.
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248 This file is a simple tabbed-delimited description of the nodes. The column names are pretty much self-explanatory. Note however that node lengths are given in k-mers. To obtain the length in nucleotides of each node you simply need to add k - 1, where k is the word-length used in velveth.
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249 The in and out columns correspond to the number of arcs on the 5' and 3' ends of the contig respectively.
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250 The coverages in columns short1 cov, short1 Ocov, short2 cov, and short2 Ocov are provided in k-mer coverage (5.1).
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251 Also, the difference between # cov and # Ocov is the way these values are computed. In the first count, slightly divergent sequences are added to the coverage tally. However, in the second, stricter count, only the sequences which map perfectly onto the consensus sequence are taken into account.
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252
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253 **LastGraph**
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254
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255 The *LastGraph* file.
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256 This file describes in its entirety the graph produced by Velvet.
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257
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258 **AMOS.afg**
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259
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260 The *velvet_asm.afg* file.
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261 This file is mainly designed to be read by the open-source AMOS genome assembly package. Nonetheless, a number of programs are available to transform this kind of file into other assembly file formats (namely ACE, TIGR, Arachne and Celera). See http://amos.sourceforge.net/ for more information.
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262 The file describes all the contigs contained in the contigs.fa file (cf 4.2.1).
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263
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264 ------
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265
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266 **Velvet parameter list**
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267
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268 This is a list of implemented Velvetg options::
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269
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270 Standard options:
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271 -cov_cutoff floating-point|auto : removal of low coverage nodes AFTER tour bus or allow the system to infer it
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272 (default: no removal)
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273 -ins_length integer : expected distance between two paired end reads (default: no read pairing)
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274 -read_trkg yes|no : tracking of short read positions in assembly (default: no tracking)
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275 -min_contig_lgth integer : minimum contig length exported to contigs.fa file (default: hash length * 2)
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276 -amos_file yes|no : export assembly to AMOS file (default: no export)
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277 -exp_cov floating point|auto : expected coverage of unique regions or allow the system to infer it
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278 (default: no long or paired-end read resolution)
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279
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280 Advanced options:
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281 -ins_length2 integer : expected distance between two paired-end reads in the second short-read dataset (default: no read pairing)
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282 -ins_length_long integer : expected distance between two long paired-end reads (default: no read pairing)
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283 -ins_length*_sd integer : est. standard deviation of respective dataset (default: 10% of corresponding length)
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284 [replace '*' by nothing, '2' or '_long' as necessary]
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285 -scaffolding yes|no : scaffolding of contigs used paired end information (default: on)
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286 -max_branch_length integer : maximum length in base pair of bubble (default: 100)
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287 -max_divergence floating-point : maximum divergence rate between two branches in a bubble (default: 0.2)
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288 -max_gap_count integer : maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
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289 -min_pair_count integer : minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)
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290 -max_coverage floating point : removal of high coverage nodes AFTER tour bus (default: no removal)
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291 -long_mult_cutoff int : minimum number of long reads required to merge contigs (default: 2)
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292 -unused_reads yes|no : export unused reads in UnusedReads.fa file (default: no)
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293
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294 Output:
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295 directory/contigs.fa : fasta file of contigs longer than twice hash length
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296 directory/stats.txt : stats file (tab-spaced) useful for determining appropriate coverage cutoff
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297 directory/LastGraph : special formatted file with all the information on the final graph
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298 directory/velvet_asm.afg : (if requested) AMOS compatible assembly file
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299
1
c397035f715d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit c5031ee00f5d61be43d2d6a1349870d6c8a817de"
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300 ]]></help>
0
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301 <expand macro="citation"/>
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302 </tool>