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comparison fastq_to_fasta.xml @ 5:8979c288aefb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_to_fasta commit 415a5c5de30530910f3039e5fc66aa15103c6f20
author iuc
date Tue, 27 Jun 2023 17:37:28 +0000
parents e282bc27be9a
children 77b41c89d856
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4:e282bc27be9a 5:8979c288aefb
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @CATS@ fastq_to_fasta 8 @CATS@ fastq_to_fasta
9 $SKIPN 9 $SKIPN
10 $RENAMESEQ 10 $RENAMESEQ
11 -v @FQQUAL@ 11 -v @FQQUAL@
12 @GZIP@ > '$output' 12 #if $compress_output == 'yes' or ($compress_output == 'infer' and ($input.ext.endswith('.gz') or $input.ext.endswith('.bz2'))):
13 | gzip -c > '$output_gz'
14 #else:
15 > '$output'
16 #end if
13 ]]></command> 17 ]]></command>
14 <inputs> 18 <inputs>
15 <expand macro="fastq_input" /> 19 <expand macro="fastq_input" />
16 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases "> 20 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
17 <option value="">yes</option> 21 <option value="">yes</option>
19 </param> 23 </param>
20 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)"> 24 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
21 <option value="-r">yes</option> 25 <option value="-r">yes</option>
22 <option value="">no</option> 26 <option value="">no</option>
23 </param> 27 </param>
28 <param name="compress_output" type="select" label="Compress output FASTA">
29 <option value="infer" selected="true">Infer from input data</option>
30 <option value="yes">Yes</option>
31 <option value="no">No</option>
32 </param>
24 </inputs> 33 </inputs>
25 <outputs> 34 <outputs>
26 <data name="output" format="fasta" metadata_source="input" /> 35 <data name="output" format="fasta" metadata_source="input" label="${tool.name} on ${on_string}: FASTA">
36 <filter>
37 compress_output == 'no' or compress_output == 'infer' and not (input.ext.endswith('.gz') or input.ext.endswith('.bz2'))
38 </filter>
39 </data>
40 <data name="output_gz" format="fasta.gz" metadata_source="input" label="${tool.name} on ${on_string}: FASTA.gz">
41 <filter>
42 compress_output == 'yes' or compress_output == 'infer' and input.ext.endswith('.gz') or input.ext.endswith('.bz2')
43 </filter>
44 </data>
27 </outputs> 45 </outputs>
28 <tests> 46 <tests>
29 <test> 47 <test expect_num_outputs="1" >
30 <!-- FASTQ-To-FASTA, keep N, don't rename --> 48 <!-- 1 FASTQ-To-FASTA, keep N, don't rename -->
31 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> 49 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
32 <param name="SKIPN" value=""/> 50 <param name="SKIPN" value=""/>
33 <param name="RENAMESEQ" value=""/> 51 <param name="RENAMESEQ" value=""/>
34 <output name="output" file="fastq_to_fasta1a.out" /> 52 <output name="output" file="fastq_to_fasta1a.out" />
35 </test> 53 </test>
36 <test> 54 <test expect_num_outputs="1" >
37 <!-- FASTQ-To-FASTA, discard N, rename --> 55 <!-- 2 FASTQ-To-FASTA, discard N, rename -->
38 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" /> 56 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
39 <param name="SKIPN" value="no"/> 57 <param name="SKIPN" value="no"/>
40 <param name="RENAMESEQ" value="yes"/> 58 <param name="RENAMESEQ" value="yes"/>
41 <output name="output" file="fastq_to_fasta1b.out" /> 59 <output name="output" file="fastq_to_fasta1b.out" />
42 </test> 60 </test>
43 <test> 61 <test expect_num_outputs="1" >
44 <!-- FASTQ-To-FASTA, discard N, rename --> 62 <!-- 3 FASTQ-To-FASTA, discard N, rename -->
45 <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" /> 63 <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" />
46 <param name="SKIPN" value="no"/> 64 <param name="SKIPN" value="no"/>
47 <param name="RENAMESEQ" value="yes"/> 65 <param name="RENAMESEQ" value="yes"/>
48 <output name="output" file="fastq_to_fasta-out2.out" /> 66 <output name="output" file="fastq_to_fasta-out2.out" />
67 </test>
68 <test expect_num_outputs="1" >
69 <!-- 4 Infer FASTQ.GZ-To-FASTA.GZ -->
70 <param name="input" value="fastq_to_fasta-in2.fastq.gz" ftype="fastqsanger.gz" />
71 <param name="SKIPN" value="no"/>
72 <param name="RENAMESEQ" value="yes"/>
73 <param name="compress_output" value="infer"/>
74 <output name="output" file="fastq_to_fasta-out2.out.gz" compare="sim_size" delta="50" />
75 </test>
76 <test expect_num_outputs="1" >
77 <!-- 5 Force FASTQ.GZ-To-FASTA -->
78 <param name="input" value="fastq_to_fasta-in2.fastq.gz" ftype="fastqsanger.gz" />
79 <param name="SKIPN" value="no"/>
80 <param name="RENAMESEQ" value="yes"/>
81 <param name="compress_output" value="no"/>
82 <output name="output" file="fastq_to_fasta-out2.out"/>
83 </test>
84 <test expect_num_outputs="1" >
85 <!-- 6 Force FASTQ-To-FASTA.GZ -->
86 <param name="input" value="fastq_to_fasta-in2.fastq" ftype="fastqsanger" />
87 <param name="SKIPN" value="no"/>
88 <param name="RENAMESEQ" value="yes"/>
89 <param name="compress_output" value="yes"/>
90 <output name="output" file="fastq_to_fasta-out2.out.gz" compare="sim_size" delta="50" />
49 </test> 91 </test>
50 </tests> 92 </tests>
51 <help><![CDATA[ 93 <help><![CDATA[
52 **What it does** 94 **What it does**
53 95