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comparison get_organelle_from_reads.xml @ 3:611219887a48 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit 00cf5ce77b828bd4cfb45df86a7334855c413497
author iuc
date Tue, 16 May 2023 09:45:40 +0000
parents 06bcf65179fb
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2:06bcf65179fb 3:611219887a48
1 <tool id="get_organelle_from_reads" name="Get organelle from reads" version="@TOOL_VERSION@"> 1 <tool id="get_organelle_from_reads" name="Get organelle from reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <macros> 2 <macros>
3 <import>macros.xml</import> 3 <import>macros.xml</import>
4 <xml name="seed_and_genes" tokens="optional"> 4 <xml name="seed_and_genes" tokens="optional">
5 <param type="data" argument="-s" format="fasta" optional="@OPTIONAL@" label="Seed sequence(s)" help="Fasta file to use as initial seed. A seed sequence in GetOrganelle is only used for identifying initial organelle reads."/> 5 <param type="data" argument="-s" format="fasta" optional="@OPTIONAL@" label="Seed sequence(s)" help="Fasta file to use as initial seed. A seed sequence in GetOrganelle is only used for identifying initial organelle reads."/>
6 <param type="data" argument="--genes" format="fasta" optional="@OPTIONAL@" label="Gene sequence(s)" help="Fasta file containing protein coding genes and ribosomal RNAs extracted from a reference genome that you want to assemble."/> 6 <param type="data" argument="--genes" format="fasta" optional="@OPTIONAL@" label="Gene sequence(s)" help="Fasta file containing protein coding genes and ribosomal RNAs extracted from a reference genome that you want to assemble."/>
14 </requirements> 14 </requirements>
15 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
16 ## Link input files 16 ## Link input files
17 #import re 17 #import re
18 #set ext = '.fastq' 18 #set ext = '.fastq'
19 #if str($fastq_input.fastq_input_selector) == 'single': 19 #if $fastq_input.fastq_input_selector == 'single':
20 #if $fastq_input.fastq_input1.ext.endswith('.gz'): 20 #if $fastq_input.fastq_input1.ext.endswith('.gz'):
21 #set ext = '.fastq.gz' 21 #set ext = '.fastq.gz'
22 #end if 22 #end if
23 #set $in1 = $fastq_input.fastq_input1 23 #set $in1 = $fastq_input.fastq_input1
24 #set $in1_name = re.sub('[^\w\-\.]', '_', str($fastq_input.fastq_input1.name)) + $ext 24 #set $in1_name = re.sub('[^\w\-\.]', '_', str($fastq_input.fastq_input1.element_identifier)) + $ext
25 ln -s '$in1' '$in1_name' && 25 ln -s '$in1' '$in1_name' &&
26 #else if str($fastq_input.fastq_input_selector) == 'paired': 26 #else if $fastq_input.fastq_input_selector == 'paired':
27 #if $fastq_input.fastq_input1.ext.endswith('.gz'): 27 #if $fastq_input.fastq_input1.ext.endswith('.gz'):
28 #set ext = '.fastq.gz' 28 #set ext = '.fastq.gz'
29 #end if 29 #end if
30 #set $in1 = $fastq_input.fastq_input1 30 #set $in1 = $fastq_input.fastq_input1
31 #set $in2 = $fastq_input.fastq_input2 31 #set $in2 = $fastq_input.fastq_input2
32 #set $in1_name = re.sub('[^\w\-\.]', '_', str($fastq_input.fastq_input1.name)) + $ext 32 #set $in1_name = re.sub('[^\w\-\.]', '_', str($fastq_input.fastq_input1.element_identifier)) + $ext
33 #set $in2_name = re.sub('[^\w\-\.]', '_', str($fastq_input.fastq_input2.name)) + $ext 33 #set $in2_name = re.sub('[^\w\-\.]', '_', str($fastq_input.fastq_input2.element_identifier)) + $ext
34 ln -s '$in1' '$in1_name' && 34 ln -s '$in1' '$in1_name' &&
35 ln -s '$in2' '$in2_name' && 35 ln -s '$in2' '$in2_name' &&
36 #else if str($fastq_input.fastq_input_selector) == 'paired_collection': 36 #else if $fastq_input.fastq_input_selector == 'paired_collection':
37 #if $fastq_input.paired_input.forward.ext.endswith('.gz'): 37 #if $fastq_input.paired_input.forward.ext.endswith('.gz'):
38 #set ext = '.fastq.gz' 38 #set ext = '.fastq.gz'
39 #end if 39 #end if
40 #set $in1 = $fastq_input.paired_input.forward 40 #set $in1 = $fastq_input.paired_input.forward
41 #set $in2 = $fastq_input.paired_input.reverse 41 #set $in2 = $fastq_input.paired_input.reverse
42 #set $in1_name = re.sub('[^\w\-\.]', '_', str($fastq_input.paired_input.name)) + $ext 42 #set $in1_name = "%s_R1%s" % (re.sub('[^\w\-\.]', '_', str($fastq_input.paired_input.element_identifier)),$ext)
43 #set $in2_name = re.sub('[^\w\-\.]', '_', str("%s_%s" % ($fastq_input.paired_input.name, "R2"))) + $ext 43 #set $in2_name = "%s_R2%s" % (re.sub('[^\w\-\.]', '_', str($fastq_input.paired_input.element_identifier)),$ext)
44 ln -s '$in1' '$in1_name' && 44 ln -s '$in1' '$in1_name' &&
45 ln -s '$in2' '$in2_name' && 45 ln -s '$in2' '$in2_name' &&
46 #end if 46 #end if
47 ## GetOrganelle cmd 47 ## GetOrganelle cmd
48 get_organelle_from_reads.py 48 get_organelle_from_reads.py
49 #if str($fastq_input.fastq_input_selector) == "single": 49 #if str($fastq_input.fastq_input_selector) == "single":
50 -u '${$in1_name}' 50 -u '$in1_name'
51 #end if 51 #end if
52 #if str($fastq_input.fastq_input_selector) == "paired": 52 #if str($fastq_input.fastq_input_selector) == "paired":
53 -1 '${$in1_name}' -2 '${$in2_name}' 53 -1 '$in1_name' -2 '$in2_name'
54 #end if 54 #end if
55 #if str($fastq_input.fastq_input_selector) == "paired_collection": 55 #if str($fastq_input.fastq_input_selector) == "paired_collection":
56 -1 '${$in1_name1}' -2 '${$in2_name}' 56 -1 '$in1_name' -2 '$in2_name'
57 #end if 57 #end if
58 -o results_directory 58 -o results_directory
59 #if str($organelle_type_input.F) == "anonym": 59 #if $organelle_type_input.F == "anonym":
60 -F '$organelle_type_input.F' 60 -F '$organelle_type_input.F'
61 -s '$organelle_type_input.s' 61 -s '$organelle_type_input.s'
62 --genes '$organelle_type_input.genes' 62 --genes '$organelle_type_input.genes'
63 #else: 63 #else:
64 -F '$organelle_type_input.F' 64 -F '$organelle_type_input.F'
128 <when value="paired"> 128 <when value="paired">
129 <param type="data" name="fastq_input1" format="fastqsanger,fastqsanger.gz" label="Forward fastq"/> 129 <param type="data" name="fastq_input1" format="fastqsanger,fastqsanger.gz" label="Forward fastq"/>
130 <param type="data" name="fastq_input2" format="fastqsanger,fastqsanger.gz" label="Reverse fastq"/> 130 <param type="data" name="fastq_input2" format="fastqsanger,fastqsanger.gz" label="Reverse fastq"/>
131 </when> 131 </when>
132 <when value="paired_collection"> 132 <when value="paired_collection">
133 <param type="data_collection" collection_type="paired" name="fastq_input1" format="fastqsanger,fastqsanger.gz" label="Paired collection fastq"/> 133 <param type="data_collection" collection_type="paired" name="paired_input" format="fastqsanger,fastqsanger.gz" label="Paired collection fastq"/>
134 </when> 134 </when>
135 </conditional> 135 </conditional>
136 <conditional name="organelle_type_input"> 136 <conditional name="organelle_type_input">
137 <param type="select" argument="-F" label="Organelle type"> 137 <param type="select" argument="-F" label="Organelle type">
138 <option value="embplant_pt" selected="true">Plant chloroplast</option> 138 <option value="embplant_pt" selected="true">Plant chloroplast</option>
230 </data> 230 </data>
231 </outputs> 231 </outputs>
232 <tests> 232 <tests>
233 <test expect_num_outputs="8"> 233 <test expect_num_outputs="8">
234 <param name="config_dir" value="getorganelle_refdata"/> 234 <param name="config_dir" value="getorganelle_refdata"/>
235 <param name="fastq_input_selector" value="paired"/> 235 <conditional name="fastq_input">
236 <param name="fastq_input1" value="Arabidopsis_simulated.10k.1.fq.gz" ftype="fastqsanger.gz"/> 236 <param name="fastq_input_selector" value="paired"/>
237 <param name="fastq_input2" value="Arabidopsis_simulated.10k.2.fq.gz" ftype="fastqsanger.gz"/> 237 <param name="fastq_input1" value="Arabidopsis_simulated.10k.1.fq.gz" ftype="fastqsanger.gz"/>
238 <param name="fastq_input2" value="Arabidopsis_simulated.10k.2.fq.gz" ftype="fastqsanger.gz"/>
239 </conditional>
238 <param name="F" value="embplant_pt" /> 240 <param name="F" value="embplant_pt" />
239 <param name="advanced" value="advanced" /> 241 <param name="advanced" value="advanced" />
240 <param name="out" value="raw_assembly_graph,simplified_graph,contig_labels,seed_fastq,seed_sam" /> 242 <param name="out" value="raw_assembly_graph,simplified_graph,contig_labels,seed_fastq,seed_sam" />
241 <assert_stdout> 243 <assert_stdout>
242 <has_text text="Thank you!" /> 244 <has_text text="Thank you!" />
244 <output name="logfile" > 246 <output name="logfile" >
245 <assert_contents> 247 <assert_contents>
246 <has_text text="Thank you!" /> 248 <has_text text="Thank you!" />
247 </assert_contents> 249 </assert_contents>
248 </output> 250 </output>
249 <output_collection name="path_sequence_list" type="list" count="2" /> 251 <output_collection name="path_sequence_list" type="list" count="2">
252 <element name="embplant_pt.K115.complete.graph1.1" ftype="fasta">
253 <assert_contents>
254 <has_n_lines n="2"/>
255 </assert_contents>
256 </element>
257 <element name="embplant_pt.K115.complete.graph1.2" ftype="fasta">
258 <assert_contents>
259 <has_n_lines n="2"/>
260 </assert_contents>
261 </element>
262 </output_collection>
250 <output name="selected_graph" > 263 <output name="selected_graph" >
251 <assert_contents> 264 <assert_contents>
252 <has_n_lines n="7" /> 265 <has_n_lines n="7" />
253 </assert_contents> 266 </assert_contents>
254 </output> 267 </output>
273 </assert_contents> 286 </assert_contents>
274 </output> 287 </output>
275 <output name="seed_sam" > 288 <output name="seed_sam" >
276 <assert_contents> 289 <assert_contents>
277 <has_text text="@HD" /> 290 <has_text text="@HD" />
291 </assert_contents>
292 </output>
293 </test>
294 <!-- Ensure paired collection works; also check output filters -->
295 <test expect_num_outputs="3">
296 <param name="config_dir" value="getorganelle_refdata"/>
297 <conditional name="fastq_input">
298 <param name="fastq_input_selector" value="paired_collection"/>
299 <param name="paired_input">
300 <collection type="paired">
301 <element name="forward" value="Arabidopsis_simulated.10k.1.fq.gz" ftype="fastqsanger.gz" />
302 <element name="reverse" value="Arabidopsis_simulated.10k.2.fq.gz" ftype="fastqsanger.gz" />
303 </collection>
304 </param>
305 </conditional>
306 <param name="F" value="embplant_pt" />
307 <param name="advanced" value="simple" />
308 <assert_stdout>
309 <has_text text="Thank you!" />
310 </assert_stdout>
311 <output name="logfile" >
312 <assert_contents>
313 <has_text text="Thank you!" />
314 </assert_contents>
315 </output>
316 <output_collection name="path_sequence_list" type="list" count="2">
317 <element name="embplant_pt.K115.complete.graph1.1" ftype="fasta">
318 <assert_contents>
319 <has_n_lines n="2"/>
320 </assert_contents>
321 </element>
322 <element name="embplant_pt.K115.complete.graph1.2" ftype="fasta">
323 <assert_contents>
324 <has_n_lines n="2"/>
325 </assert_contents>
326 </element>
327 </output_collection>
328 <output name="selected_graph" >
329 <assert_contents>
330 <has_n_lines n="7" />
278 </assert_contents> 331 </assert_contents>
279 </output> 332 </output>
280 </test> 333 </test>
281 </tests> 334 </tests>
282 <help><![CDATA[ 335 <help><![CDATA[