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comparison das_tool.xml @ 4:7d997332582e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit b32e3a4bfaf7e014097eeb0b850b61bac218802d
author iuc
date Sun, 25 Feb 2024 11:28:02 +0000
parents e23e7bf8491b
children b048a987dd7d
comparison
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3:e23e7bf8491b 4:7d997332582e
1 <tool id="das_tool" name="DAS Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="das_tool" name="DAS Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> 2 <description>for genome-resolved metagenomics</description>
3 for genome resolved metagenomics
4 </description>
5 <macros> 3 <macros>
6 <import>macros.xml</import> 4 <import>macros.xml</import>
7 </macros> 5 </macros>
8 <expand macro="biotools"/> 6 <expand macro="biotools"/>
9 <expand macro="requirements"/> 7 <expand macro="requirements"/>
17 #set $labels += "%s%s" %($sep, $s.labels) 15 #set $labels += "%s%s" %($sep, $s.labels)
18 #set $sep = "," 16 #set $sep = ","
19 #end for 17 #end for
20 18
21 #if $adv.proteins 19 #if $adv.proteins
22 ln -s $adv.proteins 'proteins' && 20 ln -s '$adv.proteins' 'proteins' &&
23 #end if 21 #end if
24 22
25 DAS_Tool 23 DAS_Tool
26 --contigs '$contigs' 24 --contigs '$contigs'
27 --outputbasename 'outputs' 25 --outputbasename 'outputs'
28 --bins '$bins' 26 --bins '$bins'
29 --labels '$labels' 27 --labels '$labels'
30 --search_engine '$adv.search_engine' 28 --search_engine '$adv.search_engine'
31 #if $adv.proteins 29 #if $adv.proteins
32 --proteins 'proteins' 30 --proteins 'proteins'
33 #end if 31 #end if
34 --score_threshold $adv.score_threshold 32 --score_threshold $adv.score_threshold
35 --duplicate_penalty $adv.duplicate_penalty 33 --duplicate_penalty $adv.duplicate_penalty
36 --megabin_penalty $adv.megabin_penalty 34 --megabin_penalty $adv.megabin_penalty
35 --max_iter_post_threshold $adv.max_iter_post_threshold
36
37 $output.write_bin_evals 37 $output.write_bin_evals
38 $output.write_bins.write_bins 38 $output.write_bins.write_bins
39 #if str($output.write_bins.write_bins) != '' 39 #if str($output.write_bins.write_bins) != ''
40 $output.write_bins.write_unbinned 40 $output.write_bins.write_unbinned
41 #end if 41 #end if
42 $output.debug 42 $output.debug
43 --threads \${GALAXY_SLOTS:-1} 43 --threads \${GALAXY_SLOTS:-1}
44 ]]></command> 44 ]]></command>
45 <inputs> 45 <inputs>
46 <param argument="--contigs" type="data" format="fasta" label="Contig sequences"/> 46 <param argument="--contigs" type="data" format="fasta" label="Contig sequences"/>
55 </param> 55 </param>
56 <param argument="--proteins" type="data" format="fasta" optional="true" label="Predicted proteins" help="The file should be prodigal fasta format: >contigID_geneNo"/> 56 <param argument="--proteins" type="data" format="fasta" optional="true" label="Predicted proteins" help="The file should be prodigal fasta format: >contigID_geneNo"/>
57 <param argument="--score_threshold" type="float" min="0" max="1" value="0.5" label="Score threshold until selection algorithm will keep selecting bins"/> 57 <param argument="--score_threshold" type="float" min="0" max="1" value="0.5" label="Score threshold until selection algorithm will keep selecting bins"/>
58 <param argument="--duplicate_penalty" type="float" min="0" max="3" value="0.6" label="Penalty for duplicate single copy genes per bin (weight b)" help="Only change if you know what you are doing"/> 58 <param argument="--duplicate_penalty" type="float" min="0" max="3" value="0.6" label="Penalty for duplicate single copy genes per bin (weight b)" help="Only change if you know what you are doing"/>
59 <param argument="--megabin_penalty" type="float" min="0" max="3" value="0.5" label="Penalty for megabins (weight c)" help="Only change if you know what you are doing"/> 59 <param argument="--megabin_penalty" type="float" min="0" max="3" value="0.5" label="Penalty for megabins (weight c)" help="Only change if you know what you are doing"/>
60 <param argument="--max_iter_post_threshold" type="integer" min="1" value="10" label="Maximum number of iterations after reaching score threshold"/>
60 </section> 61 </section>
61 <section name="output" title="Outputs"> 62 <section name="output" title="Outputs">
62 <param name="proteins" type="boolean" checked="false" label="Output predicted proteins?"/> 63 <param name="proteins" type="boolean" checked="false" label="Output predicted proteins?"/>
63 <param argument="--write_bin_evals" type="boolean" truevalue="--write_bin_evals" falsevalue="" checked="false" label="Write evaluation of input bin sets?"/> 64 <param argument="--write_bin_evals" type="boolean" truevalue="--write_bin_evals" falsevalue="" checked="false" label="Write evaluation of input bin sets?"/>
64 <conditional name="write_bins"> 65 <conditional name="write_bins">
200 @HELP_HEADER@ 201 @HELP_HEADER@
201 202
202 Inputs 203 Inputs
203 ====== 204 ======
204 205
205 - Bins: Tab separated files of contig-IDs and bin-IDs. Contigs to bin file example: :: 206 - Bins: Tab-separated files of contig-IDs and bin-IDs. Contigs to bin file example: ::
206 207
207 Contig_1 bin.01 208 Contig_1 bin.01
208 Contig_8 bin.01 209 Contig_8 bin.01
209 Contig_42 bin.02 210 Contig_42 bin.02
210 Contig_49 bin.03 211 Contig_49 bin.03
214 >Contig_1 215 >Contig_1
215 ATCATCGTCCGCATCGACGAATTCGGCGAACGAGTACCCCTGACCATCTCCGATTA... 216 ATCATCGTCCGCATCGACGAATTCGGCGAACGAGTACCCCTGACCATCTCCGATTA...
216 >Contig_2 217 >Contig_2
217 GATCGTCACGCAGGCTATCGGAGCCTCGACCCGCAAGCTCTGCGCCTTGGAGCAGG... 218 GATCGTCACGCAGGCTATCGGAGCCTCGACCCGCAAGCTCTGCGCCTTGGAGCAGG...
218 219
219 - [Optional] Proteins: Predicted proteins in prodigal fasta format. Header contains contig-ID and gene number: :: 220 - [Optional] Proteins: Predicted proteins in prodigal fasta format. The header contains contig-ID and gene number: ::
220 221
221 >Contig_1_1 222 >Contig_1_1
222 MPRKNKKLPRHLLVIRTSAMGDVAMLPHALRALKEAYPEVKVTVATKSLFHPFFEG... 223 MPRKNKKLPRHLLVIRTSAMGDVAMLPHALRALKEAYPEVKVTVATKSLFHPFFEG...
223 >Contig_1_2 224 >Contig_1_2
224 MANKIPRVPVREQDPKVRATNFEEVCYGYNVEEATLEASRCLNCKNPRCVAACPVN... 225 MANKIPRVPVREQDPKVRATNFEEVCYGYNVEEATLEASRCLNCKNPRCVAACPVN...