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annotate gfastats.xml @ 3:b70ea2e0c2dc draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
author bgruening
date Mon, 11 Jul 2022 14:12:29 +0000
parents 3e83503ac982
children d9489e014c96
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f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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1 <tool id="gfastats" name="gfastats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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2 <description>the swiss army knife for genome assembly</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="biotools"/>
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8 <version_command>gfastats --version</version_command>
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9 <command detect_errors="exit_code"><![CDATA[
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10 gfastats
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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11 '$input_file'
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12 #if $mode_condition.selector == 'statistics'
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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13 #if $mode_condition.statistics_condition.selector == 'assembly'
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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14 $mode_condition.statistics_condition.expected_genomesize
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15 #end if
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16 #end if
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17 #if $target_condition.target_option == 'true'
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18 $target_condition.target_sequence
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19 #if $target_condition.include_bed
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20 --include-bed $target_condition.include_bed
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21 #end if
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22 #if $target_condition.exclude_bed
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23 --exclude-bed $target_condition.exclude_bed
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24 #end if
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25 #end if
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26 #if $mode_condition.selector == 'manipulation'
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27 #if $mode_condition.swiss_army_knife
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28 -k $mode_condition.swiss_army_knife
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29 #end if
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30 #if $mode_condition.sort
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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31 --sort $mode_condition.sort
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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32 #end if
1
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33 #if $mode_condition.homopolymer_compress
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34 --homopolymer-compress $mode_condition.homopolymer_compress
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35 #end if
0
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36 -o dataset.$mode_condition.output_condition.out_format
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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37 #if $mode_condition.output_condition.out_format == 'fasta'
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38 #if $mode_condition.output_condition.line_length
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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39 --line-length $mode_condition.output_condition.line_length
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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40 #end if
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41 #else if $mode_condition.output_condition.out_format == 'fasta.gz'
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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42 #if $mode_condition.output_condition.line_length
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43 --line-length $mode_condition.output_condition.line_length
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44 #end if
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45 #end if
1
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46 #else if $mode_condition.selector == "statistics"
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47 #if $mode_condition.statistics_condition.selector == 'size'
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48 --out-size $mode_condition.statistics_condition.out_size
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49 #else if $mode_condition.statistics_condition.selector == 'coordinates'
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50 --out-coord $mode_condition.statistics_condition.out_coord
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51 #else if $mode_condition.statistics_condition.selector == 'assembly'
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52 --nstar-report
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53 #else
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54 --seq-report
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55 $mode_condition.statistics_condition.out_sequence
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56 #end if
3
b70ea2e0c2dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
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57 $mode_condition.discover_paths
1
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58 $mode_condition.tabular > '$stats'
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59 #else
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60 --agp-to-path $mode_condition.agp_to_path
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61 $mode_condition.discover_paths
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62 -o dataset.gfa
0
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63 #end if
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b70ea2e0c2dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
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64 --threads \${GALAXY_SLOTS:-8}
1
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65 #if $mode_condition.selector == 'manipulation' or $mode_condition.selector == 'scaffolding'
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66 && mv dataset* output_dataset
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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67 #end if
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68 ]]></command>
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69 <inputs>
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70 <param name="input_file" argument="--fasta" type="data"
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71 format="fasta,fastq,fastqsanger,gfa1,fasta.gz,fastq.gz,fastqsanger.gz,gfa1.gz"
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72 label="Input file"/>
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73 <conditional name="target_condition">
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74 <param name="target_option" type="select" label="Specify target sequences">
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75 <option value="false">Disabled</option>
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76 <option value="true">Enabled</option>
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77 </param>
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78 <when value="false"/>
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79 <when value="true">
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3e83503ac982 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
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80 <param name="target_sequence" type="text" value="" label="Target sequence" optional="true" help="Target specific sequence by header, optionally with coordinates: header[:start-end]">
0
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81 <sanitizer invalid_char="">
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82 <valid initial="string.digits,string.letters">
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83 <add value=":"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
84 <add value="-"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
85 <add value="_"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
86 <add value="|"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
87 <add value=" "/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
88 </valid>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
89 </sanitizer>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
90 <validator type="regex">[0-9A-Za-z:-_| ]+</validator>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
91 </param>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
92 <param argument="--include-bed" type="data" optional="true"
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
93 format="bed" label="Include specific intervals"
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
94 help="Generates output on a subset list of headers or coordinates
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
95 in 0-based bed format. It can be combined with --exclude-bed. Optional"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
96 <param argument="--exclude-bed" type="data" format="bed" optional="true"
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
97 label="Exclude specific intervals"
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
98 help="Exclude a subset of headers or coordinates in 0-base bed format. It can be conmbined with --include-bed Optional"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
99 </when>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
100 <when value="false"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
101 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
102 <conditional name="mode_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
103 <param name="selector" type="select" label="Tool mode">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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104 <option value="statistics">Summary statistics generation</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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105 <option value="manipulation">Genome assembly manipulation</option>
1
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
106 <option value="scaffolding">Scaffolding</option>
0
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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parents:
diff changeset
107 </param>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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parents:
diff changeset
108 <when value="manipulation">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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parents:
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109 <param argument="--swiss-army-knife" type="data"
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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110 format="text" label="SAK input file" optional="true"
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
111 help="Set of instructions provided as an ordered list"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
112 <conditional name="output_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
113 <param argument="--out-format" type="select"
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
114 label="Output format" help="Outputs selected sequences.">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
115 <option value="fasta">FASTA</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
116 <option value="fasta.gz">FASTA.gz</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
117 <option value="fastq">FASTQ</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
118 <option value="fastq.gz" selected="true">FASTQ.gz</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
119 <option value="gfa">GFA</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
120 <option value="gfa.gz">GFA.gz</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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parents:
diff changeset
121 </param>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
122 <when value="fasta">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
123 <expand macro="length_macro"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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diff changeset
124 </when>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
125 <when value="fasta.gz">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
126 <expand macro="length_macro"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
127 </when>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
128 <when value="fastq"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
129 <when value="fastq.gz"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
130 <when value="gfa"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
131 <when value="gfa.gz"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
132 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
133 <param argument="--sort" type="select" label="Sort sequences" help="Specify how to sort the sequences. Ascending/descending used the sequence/path header.">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
134 <option value="" selected="true">Disabled</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
135 <option value="ascending">Ascending</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
136 <option value="descending">Descending</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
137 <option value="largest">Largest</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
138 <option value="smallest">Smallest</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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diff changeset
139 </param>
1
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
140 <param argument="--homopolymer-compress" type="integer" min="0" value="" optional="true" label="Homopolymer compression" help="Compress all the homopolymers in the input above the given threshhold" />
0
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
141 </when>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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diff changeset
142 <when value="statistics">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
143 <conditional name="statistics_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
144 <param name="selector" type="select" label="Report mode">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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145 <option value="assembly" selected="true">Genome assembly statistics (--nstar-report)</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
146 <option value="size">Scaffold, contig or gap sizes (--out-size)</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
147 <option value="coordinates">AGP, contig or gap coordinates (--out-coord)</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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148 <option value="sequence">Sequence statistics (--seq-report)</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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diff changeset
149 </param>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
150 <when value="size">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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diff changeset
151 <param argument="--out-size" type="select" label="Feature for reporting sizes"
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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152 help="Generate a tabular file with the sequence sizes">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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153 <option value="s">Scaffolds</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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154 <option value="c">Contigs</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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155 <option value="g">Gaps</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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156 </param>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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diff changeset
157 </when>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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diff changeset
158 <when value="coordinates">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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159 <param argument="--out-coord" type="select" label="BED coordinares feature"
3
b70ea2e0c2dc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit f71fdaf79bda6704ae6dd1360406393c90026de5
bgruening
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diff changeset
160 help="Generates bed coordinates of given feature. Default: AGP">
0
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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diff changeset
161 <option value="a">AGP</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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162 <option value="c">Contigs</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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163 <option value="g">Gaps</option>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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diff changeset
164 </param>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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165 </when>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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diff changeset
166 <when value="assembly">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
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167 <param name="expected_genomesize" type="integer" min="0" optional="true"
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168 label="Expected genome size" help="Estimated genome size. This parameter is optional, but required for NG* statistics."/>
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169 </when>
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170 <when value="sequence">
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171 <param argument="--out-sequence" type="boolean" truevalue="--out-sequence" falsevalue="" checked="false"
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172 label="Report actual sequence" help="It reports also the actual sequence"/>
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173 </when>
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174 </conditional>
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175 <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true"
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176 label="Tabular-format output" help="Generate output in tabular format"/>
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177 <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly
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178 is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" />
0
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179 </when>
1
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180 <when value="scaffolding">
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181 <param argument="--agp-to-path" type="data" format="agp" label="Input AGP file" help="Integrate the AGP information into the assembly graph as paths. The scaffolding information is converted into paths through the graph" />
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182 <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly
1
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183 is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" />
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184 </when>
0
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185 </conditional>
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186 </inputs>
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187 <outputs>
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188 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats">
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189 <filter>mode_condition['selector'] == 'statistics'</filter>
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190 <change_format>
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191 <when input="tabular" value="false" format="text"/>
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192 </change_format>
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193 </data>
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194 <data name="output" format="fastq" from_work_dir="output_dataset" label="${tool.name} on ${on_string}: edited sequences">
1
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195 <filter>mode_condition['selector'] == 'manipulation' or mode_condition['selector'] == 'scaffolding'</filter>
0
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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196 <change_format>
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197 <when input="mode_condition.output_condition.out_format" value="fasta" format="fasta"/>
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198 <when input="mode_condition.output_condition.out_format" value="fasta.gz" format="fasta.gz"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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199 <when input="mode_condition.output_condition.out_format" value="fastq" format="fastq"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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200 <when input="mode_condition.output_condition.out_format" value="fastq.gz" format="fastq.gz"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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201 <when input="mode_condition.output_condition.out_format" value="gfa" format="gfa1"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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202 <when input="mode_condition.output_condition.out_format" value="gfa.gz" format="gfa1.gz"/>
1
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
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203 <when input="mode_condition.selector" value="scaffolding" format="gfa1"/>
0
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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204 </change_format>
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205 </data>
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206 </outputs>
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207 <tests>
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208 <!--Test 01 -->
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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209 <test expect_num_outputs="1">
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210 <param name="input_file" value="dataset_01.fastq.gz"/>
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211 <conditional name="target_condition">
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212 <param name="target_condition" value="true"/>
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213 <param name="target_sequence" value="S1_1"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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214 </conditional>
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215 <conditional name="mode_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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216 <param name="selector" value="manipulation"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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217 <param name="swiss_army_knife" value="swiss_army.sak"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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218 <conditional name="output_condition">
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219 <param name="out_format" value="fasta.gz"/>
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220 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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221 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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222 <output name="output" value="test_01.fasta.gz" ftype="fasta.gz"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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223 </test>
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224 <!--Test 02 -->
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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225 <test expect_num_outputs="1">
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226 <param name="input_file" value="dataset_01.fastq.gz"/>
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227 <conditional name="target_condition">
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228 <param name="target_condition" value="true"/>
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229 <param name="target_sequence" value="S1_1"/>
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230 </conditional>
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231 <conditional name="mode_condition">
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232 <param name="selector" value="statistics"/>
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233 <conditional name="statistics_condition">
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234 <param name="selector" value="size"/>
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235 <param name="out_size" value="c"/>
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236 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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237 </conditional>
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238 <output name="stats" value="test_02_stats.tabular" ftype="tabular"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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239 </test>
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240 <!--Test 03 -->
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241 <test expect_num_outputs="1">
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242 <param name="input_file" value="dataset_02.fasta.gz"/>
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243 <conditional name="mode_condition">
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244 <param name="selector" value="statistics"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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245 <conditional name="statistics_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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246 <param name="selector" value="sequence"/>
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247 </conditional>
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248 </conditional>
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diff changeset
249 <output name="stats" value="test_03_stats.tabular" ftype="tabular"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
250 </test>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
251 <!--Test 04 -->
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
252 <test expect_num_outputs="1">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
253 <param name="input_file" value="dataset_03.fasta"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
254 <conditional name="mode_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
255 <param name="selector" value="statistics"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
256 <conditional name="statistics_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
257 <param name="selector" value="assembly"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
258 <param name="expected_genomesize" value="600000"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
259 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
260 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
261 <output name="stats" value="test_04_stats.tabular" ftype="tabular"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
262 </test>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
263 <!--Test 05 -->
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
264 <test expect_num_outputs="1">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
265 <param name="input_file" value="dataset_04.gfa"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
266 <conditional name="mode_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
267 <param name="selector" value="statistics"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
268 <conditional name="statistics_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
269 <param name="selector" value="coordinates"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
270 <param name="out_coord" value="a"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
271 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
272 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
273 <output name="stats" value="test_05_stats.tabular" ftype="tabular"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
274 </test>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
275 <!--Test 06 -->
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
276 <test expect_num_outputs="1">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
277 <param name="input_file" value="dataset_04.gfa"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
278 <conditional name="mode_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
279 <param name="selector" value="manipulation"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
280 <conditional name="output_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
281 <param name="out_format" value="fasta.gz"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
282 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
283 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
284 <output name="output" value="test_06.fasta.gz" ftype="fasta.gz"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
285 </test>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
286 <!--Test 07 -->
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
287 <test expect_num_outputs="1">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
288 <param name="input_file" value="dataset_03.fasta"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
289 <conditional name="mode_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
290 <param name="selector" value="statistics"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
291 <conditional name="statistics_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
292 <param name="selector" value="assembly"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
293 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
294 <param name="tabular" value="false"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
295 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
296 <output name="stats" value="test_07_stats.tabular" ftype="tabular"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
297 </test>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
298 <!--Test 08 -->
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
299 <test expect_num_outputs="1">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
300 <param name="input_file" value="dataset_01.fastq.gz"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
301 <conditional name="mode_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
302 <param name="selector" value="manipulation"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
303 <conditional name="output_condition">
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
304 <param name="out_format" value="fasta.gz"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
305 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
306 <param name="sort" value="ascending"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
307 </conditional>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
308 <output name="output" value="test_08.fasta.gz" ftype="fasta.gz"/>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
bgruening
parents:
diff changeset
309 </test>
1
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
310 <!--Test 09 -->
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
311 <test expect_num_outputs="1">
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
312 <param name="input_file" value="dataset_03.fasta"/>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
313 <conditional name="mode_condition">
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
314 <param name="selector" value="manipulation"/>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
315 <conditional name="output_condition">
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
316 <param name="out_format" value="fasta.gz"/>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
317 </conditional>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
318 <param name="homopolymer_compress" value="10"/>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
319 </conditional>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
320 <output name="output" value="test_09.fasta.gz" ftype="fasta.gz"/>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
321 </test>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
322 <!--Test 10 -->
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
323 <test expect_num_outputs="1">
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
324 <param name="input_file" value="dataset_04.gfa"/>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
325 <conditional name="mode_condition">
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
326 <param name="selector" value="scaffolding"/>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
327 <param name="agp_to_path" value="dataset_05.agp"/>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
328 <param name="discover_paths" value="true"/>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
329 </conditional>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
330 <output name="output" value="test_10.gfa" ftype="gfa1"/>
feeebf237d03 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 8a11d204376d9daea8026f1b33a53f40fc693bf2"
bgruening
parents: 0
diff changeset
331 </test>
2
3e83503ac982 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents: 1
diff changeset
332 <!--Test 11 -->
3e83503ac982 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents: 1
diff changeset
333 <test expect_num_outputs="1">
3e83503ac982 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents: 1
diff changeset
334 <param name="input_file" value="dataset_03.fasta"/>
3e83503ac982 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents: 1
diff changeset
335 <conditional name="target_condition">
3e83503ac982 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
bgruening
parents: 1
diff changeset
336 <param name="target_option" value="true"/>
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337 <param name="include_bed" value="regions.bed"/>
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338 </conditional>
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339 <output name="stats" value="test_11_stats.tabular" ftype="tabular"/>
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340 </test>
3
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341 <!--Test 12 -->
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342 <test expect_num_outputs="1">
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343 <param name="input_file" value="dataset_04.gfa"/>
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344 <conditional name="mode_condition">
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345 <param name="selector" value="statistics"/>
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346 <conditional name="statistics_condition">
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347 <param name="selector" value="assembly"/>
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348 </conditional>
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349 <param name="tabular" value="false"/>
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350 <param name="discover_paths" value="true"/>
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351 </conditional>
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352 <output name="stats" value="test_12_stats.tabular" ftype="tabular"/>
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353 </test>
0
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354 </tests>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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355 <help><![CDATA[
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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356
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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357 .. class:: infomark
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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358
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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359 **Purpose**
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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360
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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361 gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless format conversion.
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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362
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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363
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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364 .. class:: infomark
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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365
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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366 **Metrics details**
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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367
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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368 Typical fast* metrics include:
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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369
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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370 - Scaffold, contig and gap size
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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371 - Number of scaffolds, contigs and gaps
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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372 - Total length of scaffolds, contigs and gaps
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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373 - Scaffold, contig, gap N50 and statistics (full N*/NG* statistics with the --nstar-report flag)
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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374 - Area under the curve (AuN/AuNG) values for scaffolds, contigs and gaps
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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375 - Average scaffold, contig, gap size
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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376 - Largest scaffold, contig and gap
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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377 - Base composition and GC content
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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378 - Soft-masked base counts (lower case bases)
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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379
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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380
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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381 Typical gfa metrics include:
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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382
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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383 - Number of nodes and edges
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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384 - Average degree
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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385 - Number of connected components, and length of the largets connected component
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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386 - Number of dead ends
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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387 - Number of disconnected components, and their total length
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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388
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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389
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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390 .. class:: infomark
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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391
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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392 **Assembly manipulation**
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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393
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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394 gfastats allows extensive assembly manipulation at the sequence level. Manipulation is achieved using a set of instructions provided as an ordered list in a file to the option **swiss army knife**. See the `instruction wiki <https://github.com/vgl-hub/gfastats/tree/main/instructions>`_ for a full list of instructions.
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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395
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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396 ]]></help>
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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397 <expand macro="citations" />
f9770f9a4b89 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7"
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398 </tool>