Mercurial > repos > devteam > fastq_manipulation
changeset 5:b77ecfa1664e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_manipulation commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
| author | iuc |
|---|---|
| date | Wed, 19 Feb 2020 16:55:55 +0000 |
| parents | 6f864b826b3e |
| children | ed6c5df75175 |
| files | fastq_manipulation.xml macros.xml |
| diffstat | 2 files changed, 19 insertions(+), 9 deletions(-) [+] |
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--- a/fastq_manipulation.xml Fri Nov 01 13:17:24 2019 -0400 +++ b/fastq_manipulation.xml Wed Feb 19 16:55:55 2020 +0000 @@ -1,10 +1,11 @@ -<tool id="fastq_manipulation" name="Manipulate FASTQ" version="1.1.1"> +<tool id="fastq_manipulation" name="Manipulate FASTQ" version="@TOOL_VERSION@"> <options sanitize="false" /> <!-- This tool uses a file to rely all parameter information (actually a dynamically generated python module), we can safely not sanitize any parameters --> <description>reads on various attributes</description> - <requirements> - <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <edam_topics> <edam_topic>topic_0622</edam_topic> </edam_topics> @@ -39,7 +40,7 @@ #else: #continue #end if - if not re.search(binascii.unhexlify("${ binascii.hexlify(str(match_block['match_type']['match']['match_by'])) }").decode(), search_target): + if not re.search(binascii.unhexlify(${ binascii.hexlify(str(match_block['match_type']['match']['match_by']).encode()) }).decode(), search_target): return False #end for return True @@ -51,11 +52,11 @@ #for $manipulate_block in $manipulate_blocks: #if $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'identifier': #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate': - new_read.identifier = "@%s" % new_read.identifier[1:].translate(maketrans(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])) }").decode(), binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to'])) }").decode())) + new_read.identifier = "@%s" % new_read.identifier[1:].translate(maketrans(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from']).encode()) }).decode(), binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to']).encode()) }).decode())) #end if #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'sequence': #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate': - new_read.sequence = new_read.sequence.translate(maketrans(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])) }").decode(), binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to'])) }").decode())) + new_read.sequence = new_read.sequence.translate(maketrans(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from']).encode()) }).decode(), binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to']).encode()) }).decode())) #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_comp': new_read = new_read.reverse_complement() #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'rev_no_comp': @@ -83,11 +84,11 @@ new_read = new_read.sequence_as_RNA() #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'change_adapter': if new_read.sequence_space == 'color': - new_read = new_read.change_adapter(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['new_adapter'])) }").decode()) + new_read = new_read.change_adapter(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['new_adapter']).encode()) }).decode()) #end if #elif $manipulate_block['manipulation_type']['manipulation_type_selector'] == 'quality': #if $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'translate': - new_read.quality = new_read.quality.translate(maketrans(binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])) }").decode(), binascii.unhexlify("${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to'])) }").decode())) + new_read.quality = new_read.quality.translate(maketrans(binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['from'])).encode() }).decode(), binascii.unhexlify(${ binascii.hexlify(str(manipulate_block['manipulation_type']['manipulation']['to']).encode()) }).decode())) #elif $manipulate_block['manipulation_type']['manipulation']['manipulation_selector'] == 'map_score': def score_method(score): raise Exception("Unimplemented") ##This option is not yet available, need to abstract out e.g. column adding tool action: preventing users from using 'harmful' actions
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Feb 19 16:55:55 2020 +0000 @@ -0,0 +1,9 @@ +<macros> + <token name="@TOOL_VERSION@">1.1.5</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">galaxy_sequence_utils</requirement> + <yield/> + </requirements> + </xml>> +</macros>