Mercurial > repos > greg > vsnp_sample_names
changeset 8:4f43f163c408 draft
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_sample_names commit 9f80907d5bebf572ecd34e1171751c9091cb8697"
| author | greg |
|---|---|
| date | Mon, 13 Sep 2021 19:35:10 +0000 |
| parents | e1cb13d6a82c |
| children | 8b8a3aa96833 |
| files | test-data/sample_names.txt test-data/sample_names2.txt test-data/sample_names3.txt test-data/sample_names4.txt vsnp_sample_names.xml |
| diffstat | 5 files changed, 15 insertions(+), 31 deletions(-) [+] |
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--- a/test-data/sample_names.txt Fri Sep 03 17:21:52 2021 +0000 +++ b/test-data/sample_names.txt Mon Sep 13 19:35:10 2021 +0000 @@ -1,1 +1,1 @@ -CMC_20E1 +CMC_20E1_R1_fastq_gz
--- a/test-data/sample_names2.txt Fri Sep 03 17:21:52 2021 +0000 +++ b/test-data/sample_names2.txt Mon Sep 13 19:35:10 2021 +0000 @@ -1,1 +1,1 @@ -SRR14085881 +CMC_20E1_R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_names3.txt Mon Sep 13 19:35:10 2021 +0000 @@ -0,0 +1,1 @@ +CMC_20E1_R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_names4.txt Mon Sep 13 19:35:10 2021 +0000 @@ -0,0 +1,1 @@ +SRR14085881_
--- a/vsnp_sample_names.xml Fri Sep 03 17:21:52 2021 +0000 +++ b/vsnp_sample_names.xml Mon Sep 13 19:35:10 2021 +0000 @@ -5,12 +5,11 @@ </macros> <command detect_errors="exit_code"><![CDATA[ #import difflib -#import os #import re #if $input_type_cond.input_type == 'single': #set read1 = $input_type_cond.read1 - #set sample_name = re.sub('[^\s\w\-\\.]', '_', str($read1.element_identifier)) + #set sample_name = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) #else if $input_type_cond.input_type == 'pair': #set read1 = $input_type_cond.read1 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) @@ -20,30 +19,13 @@ #set match = $matches[0] #set sample_name = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size])) #else: - #set read1 = $input_type_cond.reads_collection['forward'] - #set read1_filename = $read1.name - #set sample_name = re.sub('[^\s\w\-]', '_', str($read1_filename)) -#end if - -#if $sample_name.find('_R1') >0: - ## Something like CMC_20E1_R1.fastq.gz - #set sample_name = $sample_name.split('_R1')[0] -#else if $sample_name.find(".") > 0: - #if $read1.is_of_type('fastqsanger.gz') and $sample_name.endswith('gz'): - ## Something like my_sample.fastq.gz - #set sample_name = '.'.join($sample_name.split('.')[0:-2]) - #else: - ## Something like my_sample.fastq - #set sample_name = $os.path.splitext($sample_name)[0] - #end if -#else if $sample_name.find("_") > 0: - #if $read1.is_of_type('fastqsanger.gz') and $sample_name.endswith('gz'): - ## Something like my_sample_fastq_gz - #set sample_name = '_'.join($sample_name.split('_')[0:-2]) - #else: - ## Something like my_sample_fastq - #set sample_name = "_".join($sample_name.split("_")[0:-1]) - #end if + #set read1_name = $input_type_cond.reads_collection['forward'].name + #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1_name)) + #set read2_name = $input_type_cond.reads_collection['reverse'].name + #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2_name)) + #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks() + #set match = $matches[0] + #set sample_name = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size])) #end if echo '$sample_name' > '$output' @@ -82,7 +64,7 @@ <param name="input_type" value="pair"/> <param name="read1" value="CMC_20E1_R1.fastq.gz" dbkey="89"/> <param name="read2" value="CMC_20E1_R2.fastq.gz" dbkey="89"/> - <output name="output" file="sample_names.txt" ftype="txt"/> + <output name="output" file="sample_names2.txt" ftype="txt"/> </test> <!-- Collection of Paired reads --> <test> @@ -93,7 +75,7 @@ <element name="reverse" value="CMC_20E1_R2.fastq.gz"/> </collection> </param> - <output name="output" file="sample_names.txt" ftype="txt"/> + <output name="output" file="sample_names3.txt" ftype="txt"/> </test> <!-- Collection of Paired reads --> <test> @@ -104,7 +86,7 @@ <element name="reverse" value="SRR14085881_reverse"/> </collection> </param> - <output name="output" file="sample_names2.txt" ftype="txt"/> + <output name="output" file="sample_names4.txt" ftype="txt"/> </test> </tests> <help>