Mercurial > repos > greg > vsnp_sample_names
annotate vsnp_sample_names.xml @ 7:e1cb13d6a82c draft
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
author | greg |
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date | Fri, 03 Sep 2021 17:21:52 +0000 |
parents | fb3defef50e5 |
children | 4f43f163c408 |
rev | line source |
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3 | 1 <tool id="vsnp_sample_names" name="vSNP: sample names" version="@WRAPPER_VERSION@.1" profile="@PROFILE@"> |
0 | 2 <description></description> |
3 | 3 <macros> |
4 <import>macros.xml</import> | |
5 </macros> | |
0 | 6 <command detect_errors="exit_code"><![CDATA[ |
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e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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7 #import difflib |
0 | 8 #import os |
9 #import re | |
3 | 10 |
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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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11 #if $input_type_cond.input_type == 'single': |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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12 #set read1 = $input_type_cond.read1 |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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13 #set sample_name = re.sub('[^\s\w\-\\.]', '_', str($read1.element_identifier)) |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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14 #else if $input_type_cond.input_type == 'pair': |
3 | 15 #set read1 = $input_type_cond.read1 |
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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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16 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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17 #set read2 = $input_type_cond.read2 |
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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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18 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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19 #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks() |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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20 #set match = $matches[0] |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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21 #set sample_name = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size])) |
3 | 22 #else: |
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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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23 #set read1 = $input_type_cond.reads_collection['forward'] |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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24 #set read1_filename = $read1.name |
3 | 25 #set sample_name = re.sub('[^\s\w\-]', '_', str($read1_filename)) |
26 #end if | |
27 | |
28 #if $sample_name.find('_R1') >0: | |
29 ## Something like CMC_20E1_R1.fastq.gz | |
30 #set sample_name = $sample_name.split('_R1')[0] | |
31 #else if $sample_name.find(".") > 0: | |
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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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32 #if $read1.is_of_type('fastqsanger.gz') and $sample_name.endswith('gz'): |
3 | 33 ## Something like my_sample.fastq.gz |
34 #set sample_name = '.'.join($sample_name.split('.')[0:-2]) | |
35 #else: | |
36 ## Something like my_sample.fastq | |
37 #set sample_name = $os.path.splitext($sample_name)[0] | |
0 | 38 #end if |
3 | 39 #else if $sample_name.find("_") > 0: |
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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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40 #if $read1.is_of_type('fastqsanger.gz') and $sample_name.endswith('gz'): |
3 | 41 ## Something like my_sample_fastq_gz |
42 #set sample_name = '_'.join($sample_name.split('_')[0:-2]) | |
43 #else: | |
44 ## Something like my_sample_fastq | |
45 #set sample_name = "_".join($sample_name.split("_")[0:-1]) | |
46 #end if | |
0 | 47 #end if |
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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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48 |
3 | 49 echo '$sample_name' > '$output' |
0 | 50 ]]></command> |
51 <inputs> | |
52 <conditional name="input_type_cond"> | |
53 <param name="input_type" type="select" label="Choose the category of the files to be analyzed"> | |
3 | 54 <option value="single" selected="true">Single dataset</option> |
55 <option value="pair">Dataset pair</option> | |
56 <option value="paired">List of dataset pairs</option> | |
0 | 57 </param> |
58 <when value="single"> | |
3 | 59 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> |
0 | 60 </when> |
3 | 61 <when value="pair"> |
62 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> | |
63 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/> | |
0 | 64 </when> |
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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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65 <when value="paired"> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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66 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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67 </when> |
0 | 68 </conditional> |
69 </inputs> | |
70 <outputs> | |
3 | 71 <data name="output" format="txt"/> |
0 | 72 </outputs> |
73 <tests> | |
3 | 74 <!-- Single files --> |
0 | 75 <test> |
3 | 76 <param name="input_type" value="single"/> |
77 <param name="read1" value="CMC_20E1_R1.fastq.gz" dbkey="89"/> | |
78 <output name="output" file="sample_names.txt" ftype="txt"/> | |
79 </test> | |
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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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80 <!-- Paired reads in separate datasets --> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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81 <test> |
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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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82 <param name="input_type" value="pair"/> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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83 <param name="read1" value="CMC_20E1_R1.fastq.gz" dbkey="89"/> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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84 <param name="read2" value="CMC_20E1_R2.fastq.gz" dbkey="89"/> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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85 <output name="output" file="sample_names.txt" ftype="txt"/> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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86 </test> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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87 <!-- Collection of Paired reads --> |
3 | 88 <test> |
89 <param name="input_type" value="paired"/> | |
0 | 90 <param name="reads_collection"> |
3 | 91 <collection type="paired"> |
92 <element name="forward" value="CMC_20E1_R1.fastq.gz"/> | |
93 <element name="reverse" value="CMC_20E1_R2.fastq.gz"/> | |
0 | 94 </collection> |
95 </param> | |
3 | 96 <output name="output" file="sample_names.txt" ftype="txt"/> |
97 </test> | |
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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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98 <!-- Collection of Paired reads --> |
3 | 99 <test> |
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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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100 <param name="input_type" value="paired"/> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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101 <param name="reads_collection"> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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102 <collection type="paired"> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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103 <element name="forward" value="SRR14085881_forward"/> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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104 <element name="reverse" value="SRR14085881_reverse"/> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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105 </collection> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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106 </param> |
e1cb13d6a82c
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit f85ae0f073297ca7f5dfa22ae3a24f5fc2e6bad6"
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107 <output name="output" file="sample_names2.txt" ftype="txt"/> |
0 | 108 </test> |
109 </tests> | |
110 <help> | |
111 **What it does** | |
112 | |
3 | 113 Accepts fastqsanger sample files, extracts a unique portion of the file name as the sample name, and writes it to |
114 the output. The output text file can be consumed by the **Parse parameter value** expression tool to provide workflow | |
115 parameter values to the **Read group identifier (ID)** and the **Sample name identifier (SM)** parameters in the | |
116 **Map with BWA-MEM** tool. | |
0 | 117 </help> |
3 | 118 <expand macro="citations"/> |
0 | 119 </tool> |
120 |