Mercurial > repos > iuc > salsa

annotate salsa2.xml @ 2:ab5b7f6b7198 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 59c5c8edd0c2080d7685e312fee19de1da75097e"
author iuc
date Thu, 23 Sep 2021 19:36:12 +0000
parents ba7b0f11e470
children f77f7a7f3b83
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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>
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3 <xrefs>
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4 <xref type="bio.tools">SALSA</xref>
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5 </xrefs>
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6 <macros>
1
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7 <token name="@TOOL_VERSION@">2.3</token>
2
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8 <token name="@VERSION_SUFFIX@">1</token>
0
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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>
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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[
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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15 ln -s '$fasta_in' input.fasta &&
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16 samtools faidx input.fasta &&
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17
575b4d5bd444 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2 commit 67cd735c6709a56ad1c4d65cd84e38fccd59603b"
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18 run_pipeline.py
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19 -a '$fasta_in'
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20 -l input.fasta.fai
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21 #if $enzyme_conditional.enzyme_options == 'preconfigured':
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22 #if $enzyme_conditional.preconfigured_enzymes == 'dovetail'
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23 -e 'GATC'
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24 #else if $enzyme_conditional.preconfigured_enzymes == 'arima1'
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25 -e 'GATC,GANTC'
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26 #else
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27 -e 'GATC,GANTC,CTNAG,TTAA'
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28 #end if
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29 #else:
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30 -e '${enzyme_conditional.manual_enzyme}'
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31 #end if
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32 -b '$bed_file'
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33 #if str($cutoff):
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34 -c '$cutoff'
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35 #end if
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36 #if $gfa_file:
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37 -g '$gfa_file'
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38 #end if
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39 #if $iter:
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40 -i '$iter'
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41 #end if
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42 -o ./out
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43 ]]></command>
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44 <inputs>
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45 <param name="fasta_in" type="data" format="fasta" label="Initial assembly file" help="Headers must not contain ':'."/>
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46 <param name="bed_file" type="data" format="bed" label="Bed alignment" help="Sorted by read names"/>
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47 <param name="cutoff" argument="-c" type="integer" min="1" label="Cutoff" optional="true" help="Minimum contig length to scaffold."/>
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48 <param name="gfa_file" argument="-g" type="data" format="gfa1,gfa2" optional="true" label="Sequence graphs" help="Sequence graphs encoded in GFA format."/>
2
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49 <conditional name="enzyme_conditional">
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50 <param name="enzyme_options" type="select" label="Enzyme selection" help="TODO">
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51 <option value="preconfigured">Preconfigured restriction enzymes</option>
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52 <option value="specific">Enter a specific sequence</option>
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53 </param>
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54 <when value="preconfigured">
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55 <param name="preconfigured_enzymes" type="select" multiple="true" label="Preconfigured enzymes">
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56 <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option>
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57 <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option>
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58 <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option>
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59 </param>
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60 </when>
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61 <when value="specific">
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62 <param name="manual_enzyme" argument="-e" type="text" label="Restriction enzyme sequence(s)"
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63 help="Restriction enzyme sequence. If multiple were used, include all as a comma separated list without spaces (ex. 'GATC,AAGCTT').">
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64 <validator type="expression" message="Only alphabetical letters and the comma can be used in to define restriction enzym sequences.">value.replace(',', '').isalpha()</validator>
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65 </param>
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66 </when>
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67 </conditional>
0
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68 <param name="iter" argument="-i" type="integer" min="0" label="Iterations" optional="true" help="Number of iterations to run"/>
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69 </inputs>
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70 <outputs>
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71 <data name="scaffolds_fasta" format="fasta" from_work_dir="out/scaffolds_FINAL.fasta" label="${tool.name} on ${on_string}: FASTA assembly"/>
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72 <data name="scaffolds_agp" format="tabular" from_work_dir="out/scaffolds_FINAL.agp" label="${tool.name} on ${on_string}: agp output"/>
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="fasta_in" value="test.fasta"/>
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77 <param name="length" value="test.fai"/>
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78 <param name="bed_file" value="test.bed"/>
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79 <param name="gfa_file" value="test.gfa1"/>
2
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80 <conditional name="enzyme_conditional">
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81 <param name="enzyme_options" value="specific"/>
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82 <param name="manual_enzyme" value="GATC,GANTC"/>
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83 </conditional>
0
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84 <param name="enzyme" value="GATC,GANTC"/>
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85 <param name="cutoff" value="1000"/>
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86 <param name="iter" value="3"/>
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87 <output name="scaffolds_fasta" file="out.fasta"/>
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88 <output name="scaffolds_agp" file="out.agp"/>
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89 </test>
2
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90 <!--Test manual enzyme-->
0
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91 <test>
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92 <param name="fasta_in" value="test.fasta"/>
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93 <param name="bed_file" value="test.bed"/>
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94 <param name="gfa_file" value="test.gfa1"/>
2
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95 <conditional name="enzyme_conditional">
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96 <param name="enzyme_options" value="specific"/>
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97 <param name="manual_enzyme" value="GATC,GANTC"/>
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98 </conditional>
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99 <param name="cutoff" value="1000"/>
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100 <param name="iter" value="3"/>
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101 <output name="scaffolds_fasta" file="out.fasta"/>
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102 <output name="scaffolds_agp" file="out.agp"/>
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103 </test>
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104 <!--Test predefined enzyme-->
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105 <test>
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106 <param name="fasta_in" value="test.fasta"/>
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107 <param name="bed_file" value="test.bed"/>
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108 <param name="gfa_file" value="test.gfa1"/>
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109 <conditional name="enzyme_conditional">
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110 <param name="enzyme_options" value="preconfigured"/>
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111 <param name="preconfigured_enzymes" value="arima1"/>
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112 </conditional>
0
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113 <param name="cutoff" value="1000"/>
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114 <param name="iter" value="3"/>
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115 <output name="scaffolds_fasta" file="out.fasta"/>
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116 <output name="scaffolds_agp" file="out.agp"/>
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117 </test>
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118 </tests>
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119 <help><![CDATA[
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120 **What is does**
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121
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122 SALSA (Simple AssembLy ScAffolder) is a scaffolding tool based on a computational method that exploits the genomic proximity
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123 information in Hi-C data sets for long range scaffolding of de novo genome assemblies.
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124
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125 ]]></help>
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126 <citations>
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127 <citation type="doi">10.1101/261149</citation>
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128 <citation type="doi">10.1186/s12864-017-3879-z</citation>
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129 </citations>
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130 </tool>