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comparison dram_annotate.xml @ 2:a8ec43f1fc88 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 3234c3d93fa294fa9c2c5148eae4b399d42904d8
author iuc
date Fri, 23 Aug 2024 08:16:56 +0000
parents 3925138d40bf
children
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1:3925138d40bf 2:a8ec43f1fc88
1 <tool id="dram_annotate" name="DRAM annotate" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> 1 <tool id="dram_annotate" name="DRAM annotate" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>metagenome-assembled-genomes (MAGs)</description> 2 <description>metagenome-assembled-genomes (MAGs)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="bio_tools"/>
7 <expand macro="requirements">
8 </expand>
7 <expand macro="stdio"/> 9 <expand macro="stdio"/>
8 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
9 #import os 11 #import os
10 12
11 ## DRAM names the genbank output based on the input_fasta file name 13 ## DRAM names the genbank output based on the input_fasta file name
12 #set input_fasta_file_name = $os.path.splitext($os.path.basename(str($input_fasta)))[0] 14 #set input_fasta_file_name = $os.path.splitext($os.path.basename(str($input_fasta)))[0]
13 #set output_gbk_file_name = $input_fasta_file_name + '.gbk' 15 #set output_gbk_file_name = $input_fasta_file_name + '.gbk'
16
17 #if str($custom_hmm_dbs_cond.custom_dbs_hmm) == 'yes':
18 #for count, additional_db in enumerate($custom_hmm_dbs_cond.custom_hmm_dbs):
19 ln -s '$additional_db.custom_hmm_loc' ${count}.hmm &&
20 #end for
21 #end if
22
14 23
15 DRAM.py annotate 24 DRAM.py annotate
16 --input_fasta '$input_fasta' 25 --input_fasta '$input_fasta'
17 --output_dir 'output_dir' 26 --output_dir 'output_dir'
18 --min_contig_size $min_contig_size 27 --min_contig_size $min_contig_size
26 --custom_db_name '$additional_db.custom_db_name' 35 --custom_db_name '$additional_db.custom_db_name'
27 --custom_fasta_loc '$additional_db.custom_fasta_loc' 36 --custom_fasta_loc '$additional_db.custom_fasta_loc'
28 #end for 37 #end for
29 #end if 38 #end if
30 #if str($custom_hmm_dbs_cond.custom_dbs_hmm) == 'yes': 39 #if str($custom_hmm_dbs_cond.custom_dbs_hmm) == 'yes':
31 #for additional_db in $custom_hmm_dbs_cond.custom_hmm_dbs: 40 #for count, additional_db in enumerate($custom_hmm_dbs_cond.custom_hmm_dbs):
32 --custom_hmm_name '$additional_db.custom_hmm_name' 41 --custom_hmm_name '$additional_db.custom_hmm_name'
33 --custom_hmm_loc '$additional_db.custom_hmm_loc' 42 --custom_hmm_loc ${count}.hmm
34 #if $additional_db.custom_hmm_cutoffs_loc: 43 #if $additional_db.custom_hmm_cutoffs_loc:
35 --custom_hmm_cutoffs_loc '$additional_db.custom_hmm_cutoffs_loc' 44 --custom_hmm_cutoffs_loc '$additional_db.custom_hmm_cutoffs_loc'
36 #end if 45 #end if
37 #end for 46 #end for
38 #end if 47 #end if
50 && (test -f 'output_dir/genbank/$output_gbk_file_name' && mv 'output_dir/genbank/$output_gbk_file_name' '$output_genbank' || echo 'No genbank output produced') 59 && (test -f 'output_dir/genbank/$output_gbk_file_name' && mv 'output_dir/genbank/$output_gbk_file_name' '$output_genbank' || echo 'No genbank output produced')
51 && (test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced') 60 && (test -f 'output_dir/annotations.tsv' && mv 'output_dir/annotations.tsv' '$output_annotations' || echo 'No annotations.tsv output produced')
52 ]]></command> 61 ]]></command>
53 <inputs> 62 <inputs>
54 <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file"/> 63 <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file"/>
55 <param argument="--min_contig_size" type="integer" value="2500" min="0" label="Minimum contig size to be used for gene prediction"/> 64 <param argument="--min_contig_size" type="integer" min="0" value="2500" label="Minimum contig size to be used for gene prediction"/>
56 <param argument="--prodigal_mode" type="select" label="Select mode of prodigal to use for gene calling" help="Single mode requires genomes which are high quality with low contamination and long contigs (average length >3 Kbp)"> 65 <param argument="--prodigal_mode" type="select" label="Select mode of prodigal to use for gene calling" help="Single mode requires genomes which are high quality with low contamination and long contigs (average length &gt;3 Kbp)">
57 <option value="single" selected="true">single</option> 66 <option value="single" selected="true">single</option>
58 <option value="meta">meta</option> 67 <option value="meta">meta</option>
59 <option value="train">train</option> 68 <option value="train">train</option>
60 </param> 69 </param>
61 <param argument="--trans_table" type="integer" value="11" min="1" max="25" label="Translation table for prodigal to use for gene calling"/> 70 <param argument="--trans_table" type="integer" min="1" max="25" value="11" label="Translation table for prodigal to use for gene calling"/>
62 <param argument="--bit_score_threshold" type="integer" value="60" min="1" label="Minimum bitScore of search to retain hits"/> 71 <param argument="--bit_score_threshold" type="integer" min="1" value="60" label="Minimum bitScore of search to retain hits"/>
63 <param argument="--rbh_bit_score_threshold" type="integer" value="350" min="1" label="Minimum bitScore of reverse best hits to retain hits"/> 72 <param argument="--rbh_bit_score_threshold" type="integer" min="1" value="350" label="Minimum bitScore of reverse best hits to retain hits"/>
64 <param argument="--kofam_use_dbcan2_thresholds" type="boolean" truevalue="--kofam_use_dbcan2_thresholds" falsevalue="" checked="false" label="Use dbcan2 suggested HMM cutoffs for KOfam annotation instead of KOfam recommended cutoffs?"/> 73 <param argument="--kofam_use_dbcan2_thresholds" type="boolean" truevalue="--kofam_use_dbcan2_thresholds" falsevalue="" checked="false" label="Use dbcan2 suggested HMM cutoffs for KOfam annotation instead of KOfam recommended cutoffs?"/>
65 <conditional name="custom_fasta_dbs_cond"> 74 <conditional name="custom_fasta_dbs_cond">
66 <param name="custom_dbs_fasta" type="select" label="Specify additional fasta files against which to annotate?"> 75 <param name="custom_dbs_fasta" type="select" label="Specify additional fasta files against which to annotate?">
67 <option value="no" selected="true">No</option> 76 <option value="no" selected="true">No</option>
68 <option value="yes">Yes</option> 77 <option value="yes">Yes</option>
153 <assert_contents> 162 <assert_contents>
154 <has_text text="fasta"/> 163 <has_text text="fasta"/>
155 </assert_contents> 164 </assert_contents>
156 </output> 165 </output>
157 </test> 166 </test>
158 <!-- These settings require a db which doesn't exist in the test environment --> 167 <test>
159 <test expect_failure="true">
160 <param name="input_fasta" value="input_annotate1.fasta.gz" ftype="fasta.gz"/> 168 <param name="input_fasta" value="input_annotate1.fasta.gz" ftype="fasta.gz"/>
161 <param name="custom_dbs_fasta" value="yes"/> 169 <param name="custom_dbs_fasta" value="yes"/>
162 <repeat name="custom_fasta_dbs"> 170 <repeat name="custom_fasta_dbs">
163 <param name="custom_db_name" value="CF1"/> 171 <param name="custom_db_name" value="CF1"/>
164 <param name="custom_fasta_loc" value="annotate_custom.fasta" ftype="fasta"/> 172 <param name="custom_fasta_loc" value="annotate_custom.fasta" ftype="fasta"/>
167 <repeat name="custom_hmm_dbs"> 175 <repeat name="custom_hmm_dbs">
168 <param name="custom_hmm_name" value="CH1"/> 176 <param name="custom_hmm_name" value="CH1"/>
169 <param name="custom_hmm_loc" value="annotate_custom.hmm" ftype="hmm3"/> 177 <param name="custom_hmm_loc" value="annotate_custom.hmm" ftype="hmm3"/>
170 </repeat> 178 </repeat>
171 <param name="prodigal_mode" value="meta"/> 179 <param name="prodigal_mode" value="meta"/>
172 <assert_stderr> 180 <output name="output_genbank">
173 <has_text text="returned non-zero exit status"/> 181 <assert_contents>
174 </assert_stderr> 182 <has_text text="LOCUS"/>
183 <has_text text="gc_cont"/>
184 </assert_contents>
185 </output>
186 <output name="output_annotations">
187 <assert_contents>
188 <has_text text="fasta"/>
189 <has_text text="gene_position"/>
190 <has_n_columns n="9"/>
191 </assert_contents>
192 </output>
175 </test> 193 </test>
176 </tests> 194 </tests>
177 <help> 195 <help>
178 **What it does** 196 **What it does**
179 197