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comparison data_manager/malt_index_builder.xml @ 1:787f1ca9045a draft default tip

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author greg
date Wed, 13 Oct 2021 20:12:48 +0000
parents d69ebf52c233
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0:d69ebf52c233 1:787f1ca9045a
8 '${out_file}' 8 '${out_file}'
9 --fasta_filename '${all_fasta_source.fields.path}' 9 --fasta_filename '${all_fasta_source.fields.path}'
10 --fasta_dbkey '${all_fasta_source.fields.dbkey}' 10 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
11 --fasta_description '${all_fasta_source.fields.name}' 11 --fasta_description '${all_fasta_source.fields.name}'
12 --sequence_type '${sequence_type}' 12 --sequence_type '${sequence_type}'
13 #if str($protein_reduct_setting_cond.protein_reduct_setting) == 'yes':
14 --protein_reduct '${protein_reduct_setting_cond.protein_reduct}'
15 #end if
13 #if str($seed_setting_cond.seed_setting) == 'yes': 16 #if str($seed_setting_cond.seed_setting) == 'yes':
14 --shapes '${seed_setting_cond.shapes}' 17 --shapes '${seed_setting_cond.shapes}'
15 --max_hits_per_seed $seed_setting_cond.max_hits_per_seed 18 ## malt-build requires a string here.
16 --protein_reduct '${seed_setting_cond.protein_reduct}' 19 --max_hits_per_seed '${seed_setting_cond.max_hits_per_seed}'
17 #end if 20 #end if
18 ]]></command> 21 ]]></command>
19 <inputs> 22 <inputs>
20 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> 23 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
21 <options from_data_table="all_fasta"/> 24 <options from_data_table="all_fasta"/>
22 </param> 25 </param>
23 <param name="sequence_name" type="text" value="" label="Name of sequence" /> 26 <param name="sequence_name" type="text" value="" label="Name of sequence"/>
24 <param name="sequence_id" type="text" value="" label="ID for sequence" /> 27 <param name="sequence_id" type="text" value="" label="ID for sequence"/>
25 <param name="sequence_type" type="select" label="Specify whether the reference sequences are DNA or Protein sequences" help="Use the DNA setting For RNA sequences"> 28 <param name="sequence_type" type="select" label="Reference sequences type" help="Use the DNA setting For RNA sequences">
26 <option value="DNA" selected="true">DNA</option> 29 <option value="DNA" selected="true">DNA</option>
27 <option value="Protein">Protein</option> 30 <option value="Protein">Protein</option>
28 </param> 31 </param>
29 <conditional name="seed_setting_cond"> 32 <conditional name="protein_reduct_setting_cond">
30 <param name="seed_setting" type="select" label="Specify seed settings?"> 33 <param name="protein_reduct_setting" type="select" label="Specify protein alphabet resuction?" help="Used only if the reference sequences are Protein sequences">
31 <option selected="true" value="no">No</option> 34 <option selected="true" value="no">No</option>
32 <option value="yes">Yes</option> 35 <option value="yes">Yes</option>
33 </param> 36 </param>
34 <when value="no"/> 37 <when value="no"/>
35 <when value="yes"> 38 <when value="yes">
36 <param name="shapes" type="text" value="" label="Comma-separated list of seed shapes" help="See help text below">
37 <sanitizer invalid_char="">
38 <valid initial="string.printable">
39 <remove value="&apos;" />
40 </valid>
41 <mapping initial="none">
42 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
43 </mapping>
44 </sanitizer>
45 </param>
46 <param name="max_hits_per_seed" type="integer" value="1" min="1" label="Maximum number of hits per seed"/>
47 <param name="protein_reduct" type="select" label="Name or definition of protein alphabet reduction"> 39 <param name="protein_reduct" type="select" label="Name or definition of protein alphabet reduction">
48 <option selected="true" value="DIAMOND_11">DIAMOND_11</option> 40 <option selected="true" value="DIAMOND_11">DIAMOND_11</option>
49 <option value="BLOSUM50_10">BLOSUM50_10</option> 41 <option value="BLOSUM50_10">BLOSUM50_10</option>
50 <option value="BLOSUM50_11">BLOSUM50_11</option> 42 <option value="BLOSUM50_11">BLOSUM50_11</option>
51 <option value="BLOSUM50_15">BLOSUM50_15</option> 43 <option value="BLOSUM50_15">BLOSUM50_15</option>
57 <option value="SDM12">SDM12</option> 49 <option value="SDM12">SDM12</option>
58 <option value="UNREDUCED">UNREDUCED</option> 50 <option value="UNREDUCED">UNREDUCED</option>
59 </param> 51 </param>
60 </when> 52 </when>
61 </conditional> 53 </conditional>
54 <conditional name="seed_setting_cond">
55 <param name="seed_setting" type="select" label="Specify seed settings?">
56 <option selected="true" value="no">No</option>
57 <option value="yes">Yes</option>
58 </param>
59 <when value="no"/>
60 <when value="yes">
61 <param name="shapes" type="text" value="" label="Comma-separated list of seed shapes" help="See help text below">
62 <sanitizer invalid_char="">
63 <valid initial="string.printable">
64 <remove value="&apos;"/>
65 </valid>
66 <mapping initial="none">
67 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
68 </mapping>
69 </sanitizer>
70 </param>
71 <param name="max_hits_per_seed" type="integer" value="1" min="1" label="Maximum number of hits per seed"/>
72 </when>
73 </conditional>
62 </inputs> 74 </inputs>
63 <outputs> 75 <outputs>
64 <data name="out_file" format="data_manager_json" /> 76 <data name="out_file" format="data_manager_json"/>
65 </outputs> 77 </outputs>
66 <tests> 78 <tests>
67 <test> 79 <test>
68 <param name="all_fasta_source" value="phiX174"/> 80 <param name="all_fasta_source" value="phiX174"/>
69 <output name="out_file" value="malt_index_builder.json"/> 81 <param name="sequence_name" value="Pretty name for phiX174"/>
82 <param name="sequence_id" value="phiX174-1"/>
83 <output name="out_file" value="malt_index_builder1.json"/>
84 </test>
85 <test>
86 <param name="all_fasta_source" value="phiX174"/>
87 <param name="sequence_name" value="Pretty name for phiX174"/>
88 <param name="sequence_id" value="phiX174-1"/>
89 <param name="seed_setting" value="yes"/>
90 <param name="shapes" value="111110111011110110111111"/>
91 <output name="out_file" value="malt_index_builder1.json"/>
92 </test>
93 <test>
94 <param name="all_fasta_source" value="phiX174"/>
95 <param name="sequence_name" value="Pretty name for phiX174"/>
96 <param name="sequence_id" value="phiX174-2"/>
97 <param name="sequence_type" value="Protein"/>
98 <param name="protein_reduct_setting" value="yes"/>
99 <param name="protein_reduct" value="BLOSUM50_10"/>
100 <output name="out_file" value="malt_index_builder2.json"/>
70 </test> 101 </test>
71 </tests> 102 </tests>
72 <help> 103 <help>
73 .. class:: infomark 104 .. class:: infomark
74 105
75 **Notice:** Values for name, description, and id will be generated automatically if left blank. 106 **Notice:** Values for Name and ID of sequence will be generated automatically if left blank.
76 107
77 **What it does** 108 **What it does**
78 109
79 Takes a reference sequence database (represented by a FastA file, possibly in gzip format) as input and produces an index that 110 Takes a reference sequence database (represented by a FastA file, possibly in gzip format) as input and produces an index that
80 can be used by the malt tool as input. If MALT is to be used as a taxonomic and/or functional analysis tool as well as an 111 can be used by the malt tool as input. If MALT is to be used as a taxonomic and/or functional analysis tool as well as an