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comparison instagraal.xml @ 1:8d5b13b571fd draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/instagraal commit 3005cec91ca52f9d28aa2fe0bd4190555abafc35
author bgruening
date Sun, 13 Nov 2022 12:59:17 +0000
parents 23d20e5e427d
children d1be552c6034
comparison
equal deleted inserted replaced
0:23d20e5e427d 1:8d5b13b571fd
26 mkdir -p ./outputs/ && 26 mkdir -p ./outputs/ &&
27 ln -s '$abs_fragments_contacts_weighted' hic_folder/abs_fragments_contacts_weighted.txt && 27 ln -s '$abs_fragments_contacts_weighted' hic_folder/abs_fragments_contacts_weighted.txt &&
28 ln -s '$fragments_list' hic_folder/fragments_list.txt && 28 ln -s '$fragments_list' hic_folder/fragments_list.txt &&
29 ln -s '$info_contigs' hic_folder/info_contigs.txt && 29 ln -s '$info_contigs' hic_folder/info_contigs.txt &&
30 30
31 #if $reference_genome.source == 'history': 31 #if $ref_source.source == "history"
32 #set $ref_genome = 'reference.fasta' 32 #set $ref_genome = 'reference.fasta'
33 ln -s -f '${reference_genome.history_item}' $ref_genome && 33 ln -s '${ref_source.ref_fasta}' $ref_genome &&
34 #else: 34 #elif $ref_source.source == "builtin"
35 #set $ref_genome = $reference_genome.index.fields.path 35 #set $ref_genome = '${ref_source.ref_fasta_builtin.fields.path}'
36 #end if 36 #end if
37 37
38 instagraal 38 instagraal
39 ./hic_folder 39 ./hic_folder
40 $ref_genome 40 $ref_genome
68 68
69 <param name="abs_fragments_contacts_weighted" type="data" format="tabular" label="Abs fragments contacts weighted"/> 69 <param name="abs_fragments_contacts_weighted" type="data" format="tabular" label="Abs fragments contacts weighted"/>
70 <param name="fragments_list" type="data" format="tabular" label="Fragments list"/> 70 <param name="fragments_list" type="data" format="tabular" label="Fragments list"/>
71 <param name="info_contigs" type="data" format="tabular" label="info_contigs"/> 71 <param name="info_contigs" type="data" format="tabular" label="info_contigs"/>
72 72
73 <conditional name="reference_genome"> 73 <conditional name="ref_source">
74 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options."> 74 <param type="select" name="source" label="Reference genome source">
75 <option value="indexed" selected="true">Use a built-in genome</option> 75 <option value="history" selected="true">History</option>
76 <option value="history">Use a genome from history</option> 76 <option value="builtin">Built-in</option>
77 </param> 77 </param>
78 <when value="indexed"> 78 <when value="history">
79 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team."> 79 <param type="data" format="fasta" name="ref_fasta" label="Reference genome" />
80 <options from_data_table="fasta_indexes"> 80 </when>
81 <filter type="sort_by" column="2" /> 81 <when value="builtin">
82 <validator type="no_options" message="No genomes are available for the selected input dataset" /> 82 <param type="select" name="ref_fasta_builtin" label="Reference genome">
83 </options> 83 <options from_data_table="all_fasta" />
84 </param> 84 </param>
85 </when>
86 <when value="history">
87 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
88 </when> 85 </when>
89 </conditional> 86 </conditional>
90 87
91 <param argument="--level" type="integer" value="4" min="3" max="6" label="Level (resolution) of the contact map" 88 <param argument="--level" type="integer" value="4" min="3" max="6" label="Level (resolution) of the contact map"
92 help="Increasing level by one means a threefold smaller resolution but also a threefold faster computation time."/> 89 help="Increasing level by one means a threefold smaller resolution but also a threefold faster computation time."/>
114 <tests> 111 <tests>
115 <test> 112 <test>
116 <param name="abs_fragments_contacts_weighted" value="abs_fragments_contacts_weighted.tabular" /> 113 <param name="abs_fragments_contacts_weighted" value="abs_fragments_contacts_weighted.tabular" />
117 <param name="fragments_list" value="fragments_list.tabular" /> 114 <param name="fragments_list" value="fragments_list.tabular" />
118 <param name="info_contigs" value="info_contigs.tabular" /> 115 <param name="info_contigs" value="info_contigs.tabular" />
119 <conditional name="reference_genome"> 116 <conditional name="ref_source">
120 <param name="source" value="history"/> 117 <param name="source" value="history"/>
121 <param name="history_item" value="fake.fasta" /> 118 <param name="ref_fasta" value="fake.fasta" />
122 </conditional> 119 </conditional>
123 <assert_command> 120 <assert_command>
124 <has_text text="NNNNNNNNNN"/> <!-- 10 long, the default --> 121 <has_text text="NNNNNNNNNN"/> <!-- 10 long, the default -->
125 <not_has_text text="NNNNNNNNNNN"/> <!-- too long --> 122 <not_has_text text="NNNNNNNNNNN"/> <!-- too long -->
126 <has_text text="--cycles 30" /> 123 <has_text text="--cycles 30" />