|
2 | 2 | <description>Compare multiple runs of long read sequencing data and alignments</description> |
3 | 3 | <macros> |
4 | 4 | <token name="@TOOL_VERSION@">1.25.6</token> |
5 | | - <token name="@VERSION_SUFFIX@">0</token> |
| 5 | + <token name="@VERSION_SUFFIX@">1</token> |
6 | 6 | </macros> |
7 | 7 | <xrefs> |
8 | 8 | <xref type="bio.tools">nanocomp</xref> |
|
13 | 13 | <version_command>NanoComp -v</version_command> |
14 | 14 | <command detect_errors="exit_code"><![CDATA[ |
15 | 15 | #import re |
16 | | - ##link input file with names |
| 16 | +
|
| 17 | + ##link input files with proper names |
| 18 | + #set $linked_files = [] |
17 | 19 | #for $file in $inputs.input_type.input_data |
18 | | - #if '.' in str($file.name) |
19 | | - #set $in_name = re.sub('[\-\:\s]', '_', str($file.name)) |
20 | | - #else |
21 | | - #set $in_name = re.sub('[\-\:\s]', '_', str($file.name)) + "." + $file.ext |
22 | | - #end if |
23 | | - ln -sf $file $in_name && |
| 20 | + #if '.' in str($file.name) |
| 21 | + #set $in_name = re.sub('[\-\:\s]', '_', str($file.name)) |
| 22 | + #else |
| 23 | + #set $in_name = re.sub('[\-\:\s]', '_', str($file.name)) + "." + $file.ext |
| 24 | + #end if |
| 25 | + ln -sf '$file' '$in_name' && |
| 26 | + #silent $linked_files.append($in_name) |
24 | 27 | #end for |
25 | 28 |
|
26 | 29 | ##run nanocomp |
|
51 | 54 | --arrow |
52 | 55 | #end if |
53 | 56 |
|
54 | | - #for $file in $inputs.input_type.input_data |
55 | | - #if '.' in str($file.name) |
56 | | - #set $in_name = re.sub('[\-\:\s]', '_', str($file.name)) |
57 | | - #else |
58 | | - #set $in_name = re.sub('[\-\:\s]', '_', str($file.name)) + "." + $file.ext |
59 | | - #end if |
60 | | - $in_name |
| 57 | + ## add the input files |
| 58 | + #for $file in $linked_files |
| 59 | + '$file' |
61 | 60 | #end for |
62 | 61 |
|
63 | 62 | ##Filter options |
|
108 | 107 | <option value="arrow">ARROW files</option> |
109 | 108 | </param> |
110 | 109 | <when value="fastq"> |
111 | | - <param name="input_data" type="data" format="fastq,fastq.gz" multiple="true" label="FASTQ input files" help="Data is in (compressed) fastq format" /> |
| 110 | + <param name="input_data" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="FASTQ input files" help="Data is in (compressed) fastq format" /> |
112 | 111 | </when> |
113 | 112 | <when value="fastq_r"> |
114 | | - <param name="input_data" type="data" format="fastq,fastq.gz" multiple="true" label="FASTQ input files" help="Data is in one or more fastq file(s) generated by MinKNOW or guppy with additional information concerning channel and time" /> |
| 113 | + <param name="input_data" type="data" format="fastqsanger,fastqsanger.gz" multiple="true" label="FASTQ input files" help="Data is in one or more fastq file(s) generated by MinKNOW or guppy with additional information concerning channel and time" /> |
115 | 114 | </when> |
116 | 115 | <when value="fasta"> |
117 | 116 | <param name="input_data" type="data" format="fasta,fasta.gz" multiple="true" label="FASTA input files" help="Data is in (compressed) fasta format" /> |
|
164 | 163 | <data name="html_report" format="html" from_work_dir="NanoComp-report.html" label="${tool.name} on ${on_string}: Html Report"/> |
165 | 164 | </outputs> |
166 | 165 | <tests> |
| 166 | + <!-- 1) fastq input --> |
167 | 167 | <test expect_num_outputs="3"> |
168 | 168 | <section name="inputs"> |
169 | 169 | <conditional name="input_type"> |
|
183 | 183 | </assert_contents> |
184 | 184 | </output> |
185 | 185 | </test> |
| 186 | + <!-- 2) bam input --> |
186 | 187 | <test expect_num_outputs="3"> |
187 | 188 | <section name="inputs"> |
188 | 189 | <conditional name="input_type"> |
|
201 | 202 | </assert_contents> |
202 | 203 | </output> |
203 | 204 | </test> |
| 205 | + <!-- 3) fastq input, tsv output --> |
204 | 206 | <test expect_num_outputs="3"> |
205 | 207 | <section name="inputs"> |
206 | 208 | <conditional name="input_type"> |
|
217 | 219 | </assert_contents> |
218 | 220 | </output> |
219 | 221 | </test> |
| 222 | + <!-- 4) bam input, box plot output --> |
220 | 223 | <test expect_num_outputs="3"> |
221 | 224 | <section name="inputs"> |
222 | 225 | <conditional name="input_type"> |
|
0 commit comments