Mercurial > repos > bgruening > instagraal
comparison instagraal.xml @ 1:8d5b13b571fd draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/instagraal commit 3005cec91ca52f9d28aa2fe0bd4190555abafc35
author | bgruening |
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date | Sun, 13 Nov 2022 12:59:17 +0000 |
parents | 23d20e5e427d |
children | d1be552c6034 |
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0:23d20e5e427d | 1:8d5b13b571fd |
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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" /> |