Mercurial > repos > iuc > salsa

annotate salsa2.xml @ 0:575b4d5bd444 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
author iuc
date Sun, 17 Jan 2021 13:24:22 +0000
parents
children ba7b0f11e470
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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1 <tool id="salsa" name="SALSA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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2 <description>scaffold long read assemblies with Hi-C</description>
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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3 <xrefs>
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4 <xref type="bio.tools">SALSA</xref>
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5 </xrefs>
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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6 <macros>
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7 <token name="@TOOL_VERSION@">2.2</token>
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8 <token name="@VERSION_SUFFIX@">0</token>
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9 </macros>
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">salsa2</requirement>
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12 <requirement type="package" version="1.11">samtools</requirement>
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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13 </requirements>
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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14 <command detect_errors="exit_code"><![CDATA[
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15 ln -s '$fasta_in' input.fasta &&
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16 samtools faidx input.fasta &&
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17
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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18 run_pipeline.py
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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19 -a '$fasta_in'
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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20 -l input.fasta.fai
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21 -b '$bed_file'
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22 -e '$enzyme'
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23
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24 #if str($cutoff):
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25 -c '$cutoff'
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26 #end if
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27 #if $gfa_file:
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28 -g '$gfa_file'
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29 #end if
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30 #if $iter:
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31 -i '$iter'
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32 #end if
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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33 -o ./out
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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34 ]]></command>
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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35 <inputs>
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36 <param name="fasta_in" type="data" format="fasta" label="Initial assembly file" help="Headers must not contain ':'."/>
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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37 <param name="bed_file" type="data" format="bed" label="Bed alignment" help="Sorted by read names"/>
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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38 <param name="cutoff" argument="-c" type="integer" min="1" label="Cutoff" optional="true" help="Minimum contig length to scaffold."/>
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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39 <param name="gfa_file" argument="-g" type="data" format="gfa1,gfa2" optional="true" label="Sequence graphs" help="Sequence graphs encoded in GFA format."/>
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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40 <param name="enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)"
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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41 help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT').">
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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42 <validator type="expression" message="Only alphabetical letters and the comma can be used in to define restriction enzym sequences.">value.replace(',', '').isalpha()</validator>
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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43 </param>
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44 <param name="iter" argument="-i" type="integer" min="0" label="Iterations" optional="true" help="Number of iterations to run"/>
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45 </inputs>
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46 <outputs>
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47 <data name="scaffolds_fasta" format="fasta" from_work_dir="out/scaffolds_FINAL.fasta" label="${tool.name} on ${on_string}: FASTA assembly"/>
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48 <data name="scaffolds_agp" format="tabular" from_work_dir="out/scaffolds_FINAL.agp" label="${tool.name} on ${on_string}: agp output"/>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="fasta_in" value="test.fasta"/>
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53 <param name="length" value="test.fai"/>
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54 <param name="bed_file" value="test.bed"/>
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55 <param name="gfa_file" value="test.gfa1"/>
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56 <param name="enzyme" value="GATC,GANTC"/>
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57 <param name="cutoff" value="1000"/>
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58 <param name="iter" value="3"/>
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59 <output name="scaffolds_fasta" file="out.fasta"/>
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60 <output name="scaffolds_agp" file="out.agp"/>
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61 </test>
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62 <test>
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63 <param name="fasta_in" value="test.fasta"/>
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64 <param name="bed_file" value="test.bed"/>
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65 <param name="gfa_file" value="test.gfa1"/>
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66 <param name="enzyme" value="GATC,GANTC"/>
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67 <param name="cutoff" value="1000"/>
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68 <param name="iter" value="3"/>
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69 <output name="scaffolds_fasta" file="out.fasta"/>
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70 <output name="scaffolds_agp" file="out.agp"/>
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74 **What is does**
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75
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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76 SALSA (Simple AssembLy ScAffolder) is a scaffolding tool based on a computational method that exploits the genomic proximity
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77 information in Hi-C data sets for long range scaffolding of de novo genome assemblies.
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78
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79 ]]></help>
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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80 <citations>
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81 <citation type="doi">10.1101/261149</citation>
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82 <citation type="doi">10.1186/s12864-017-3879-z</citation>
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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83 </citations>
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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84 </tool>