| Previous changeset 16:dba489bfcd62 (2019-12-02) Next changeset 18:63dd26468588 (2021-07-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 4812c313fd8762b11f7fd002436e3a93b4c67f00" |
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modified:
emboss_dreg.xml emboss_format_corrector.py emboss_preg.xml macros.xml |
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added:
test-data/dreg.seqtable test-data/preg.seqtable |
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| diff -r dba489bfcd62 -r ce385837c160 emboss_dreg.xml --- a/emboss_dreg.xml Mon Dec 02 21:13:50 2019 -0500 +++ b/emboss_dreg.xml Fri Nov 20 16:51:11 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: dreg27" name="dreg" version="@VERSION@"> +<tool id="EMBOSS: dreg27" name="dreg" version="@VERSION@+galaxy1"> <description>Regular expression search of a nucleotide sequence</description> <macros> <import>macros.xml</import> @@ -7,12 +7,20 @@ <command>dreg -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto</command> <inputs> <param name="input1" type="data" format="data" label="Sequence 1" /> - <param name="pattern" type="text" value="(AUG)" label="Regular expression pattern" /> + <param name="pattern" type="text" value="(AUG)" label="Regular expression pattern"> + <expand macro="regex_sanitizer"/> + </param> </inputs> <outputs> <data name="out_file1" format="dreg" /> </outputs> - <!-- tests not possible since dreg timestamps output file --> + <tests> + <test> + <param name="input1" ftype="fasta" value="2.fasta"/> + <param name="pattern" value="g[atcg]ctct{2,2}gcc"/> + <output name="out_file1" value="dreg.seqtable" lines_diff="8"/> + </test> + </tests> <help> You can view the original documentation here_. |
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| diff -r dba489bfcd62 -r ce385837c160 emboss_format_corrector.py --- a/emboss_format_corrector.py Mon Dec 02 21:13:50 2019 -0500 +++ b/emboss_format_corrector.py Fri Nov 20 16:51:11 2020 +0000 |
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| @@ -3,7 +3,7 @@ # Properly set file formats before job run -def exec_before_job( app, inp_data=None, out_data=None, tool=None, param_dict=None ): +def exec_before_job(app, inp_data=None, out_data=None, tool=None, param_dict=None): # why isn't items an ordered list? items = out_data.items() items = sorted(items, key=operator.itemgetter(0)) @@ -11,7 +11,7 @@ # normal filetype correction data_count = 1 for name, data in items: - outputType = param_dict.get( 'out_format' + str(data_count), None ) + outputType = param_dict.get('out_format' + str(data_count), None) if outputType is not None: if outputType == 'ncbi': outputType = "fasta" @@ -20,28 +20,28 @@ elif outputType == 'text': outputType = "txt" data = app.datatypes_registry.change_datatype(data, outputType) - app.model.context.add( data ) + app.model.context.add(data) app.model.context.flush() data_count += 1 # html filetype correction data_count = 1 for name, data in items: - wants_plot = param_dict.get( 'html_out' + str(data_count), None ) + wants_plot = param_dict.get('html_out' + str(data_count), None) ext = "html" if wants_plot == "yes": data = app.datatypes_registry.change_datatype(data, ext) - app.model.context.add( data ) + app.model.context.add(data) app.model.context.flush() data_count += 1 # png file correction data_count = 1 for name, data in items: - wants_plot = param_dict.get( 'plot' + str(data_count), None ) + wants_plot = param_dict.get('plot' + str(data_count), None) ext = "png" if wants_plot == "yes": data = app.datatypes_registry.change_datatype(data, ext) - app.model.context.add( data ) + app.model.context.add(data) app.model.context.flush() data_count += 1 |
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| diff -r dba489bfcd62 -r ce385837c160 emboss_preg.xml --- a/emboss_preg.xml Mon Dec 02 21:13:50 2019 -0500 +++ b/emboss_preg.xml Fri Nov 20 16:51:11 2020 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="EMBOSS: preg78" name="preg" version="@VERSION@"> +<tool id="EMBOSS: preg78" name="preg" version="@VERSION@+galaxy1"> <description>Regular expression search of a protein sequence</description> <macros> <import>macros.xml</import> @@ -7,11 +7,20 @@ <command>preg -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -auto</command> <inputs> <param name="input1" type="data" format="data" label="Sequence" /> - <param name="pattern" type="text" value="(ACD)" label="Regular expression pattern" /> + <param name="pattern" type="text" value="(ACD)" label="Regular expression pattern"> + <expand macro="regex_sanitizer"/> + </param> </inputs> <outputs> <data name="out_file1" format="preg" /> </outputs> + <tests> + <test> + <param name="input1" ftype="fasta" value="2.pep"/> + <param name="pattern" value="AS-?L"/> + <output name="out_file1" value="preg.seqtable" lines_diff="8"/> + </test> + </tests> <help> You can view the original documentation here_. |
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| diff -r dba489bfcd62 -r ce385837c160 macros.xml --- a/macros.xml Mon Dec 02 21:13:50 2019 -0500 +++ b/macros.xml Fri Nov 20 16:51:11 2020 +0000 |
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| @@ -19,4 +19,27 @@ <yield /> </citations> </xml> + <xml name="regex_sanitizer"> + <sanitizer> + <valid initial="string.ascii_letters,string.digits"> + <add value="^"/> + <add value="$"/> + <add value="("/> + <add value=")"/> + <add value="|"/> + <add value="?"/> + <add value="*"/> + <add value="+"/> + <add value="{"/> + <add value="}"/> + <add value="\"/> + <add value="["/> + <add value="]"/> + <add value="."/> + <add value=","/> + </valid> + </sanitizer> + <validator type="empty_field" /> + <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator> + </xml> </macros> |
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| diff -r dba489bfcd62 -r ce385837c160 test-data/dreg.seqtable --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dreg.seqtable Fri Nov 20 16:51:11 2020 +0000 |
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| @@ -0,0 +1,34 @@ +######################################## +# Program: dreg +# Rundate: Thu 19 Nov 2020 16:17:07 +# Commandline: dreg +# -sequence /tmp/tmpo6m2ny4d/files/4/b/a/dataset_4ba37f85-26f4-4d07-82eb-e313af066380.dat +# -outfile /tmp/tmpo6m2ny4d/files/4/6/e/dataset_46e9ea4f-becf-4442-9075-66c0be3bf67f.dat +# -pattern "g[atcg]ctct{2,2}gcc" +# -raccshow3 no +# -rusashow3 no +# -rdesshow3 no +# -auto +# Report_format: seqtable +# Report_file: /tmp/tmpo6m2ny4d/files/4/6/e/dataset_46e9ea4f-becf-4442-9075-66c0be3bf67f.dat +######################################## + +#======================================= +# +# Sequence: Sequence from: 1 to: 561 +# HitCount: 1 +# +# Pattern: g[atcg]ctct{2,2}gcc +# +#======================================= + + Start End Pattern_name Sequence + 141 150 regex1 gtctcttgcc + +#--------------------------------------- +#--------------------------------------- + +#--------------------------------------- +# Total_sequences: 1 +# Total_hitcount: 1 +#--------------------------------------- |
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| diff -r dba489bfcd62 -r ce385837c160 test-data/preg.seqtable --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/preg.seqtable Fri Nov 20 16:51:11 2020 +0000 |
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| @@ -0,0 +1,87 @@ +######################################## +# Program: preg +# Rundate: Thu 19 Nov 2020 16:17:17 +# Commandline: preg +# -sequence /tmp/tmpo6m2ny4d/files/f/6/0/dataset_f609b47c-0fca-4ed4-b83a-d3263a8cfb17.dat +# -outfile /tmp/tmpo6m2ny4d/files/7/0/8/dataset_7087e30b-2929-4100-b6d7-1220864626f8.dat +# -pattern "ASX?L" +# -auto +# Report_format: seqtable +# Report_file: /tmp/tmpo6m2ny4d/files/7/0/8/dataset_7087e30b-2929-4100-b6d7-1220864626f8.dat +######################################## + +#======================================= +# +# Sequence: HSFAU1_3 from: 1 to: 150 +# HitCount: 1 +# +# Pattern: ASX?L +# +#======================================= + + Start End Pattern_name Sequence + 47 49 regex1 ASL + +#--------------------------------------- +#--------------------------------------- +#======================================= +# +# Sequence: HSFAU2_3 from: 1 to: 78 +# HitCount: 1 +# +# Pattern: ASX?L +# +#======================================= + + Start End Pattern_name Sequence + 47 49 regex1 ASL + +#--------------------------------------- +#--------------------------------------- +#======================================= +# +# Sequence: HSFAU3_3 from: 1 to: 151 +# HitCount: 1 +# +# Pattern: ASX?L +# +#======================================= + + Start End Pattern_name Sequence + 47 49 regex1 ASL + +#--------------------------------------- +#--------------------------------------- +#======================================= +# +# Sequence: HSFAU4_3 from: 1 to: 153 +# HitCount: 1 +# +# Pattern: ASX?L +# +#======================================= + + Start End Pattern_name Sequence + 48 50 regex1 ASL + +#--------------------------------------- +#--------------------------------------- +#======================================= +# +# Sequence: HSFAU5_3 from: 1 to: 151 +# HitCount: 1 +# +# Pattern: ASX?L +# +#======================================= + + Start End Pattern_name Sequence + 47 49 regex1 ASL + +#--------------------------------------- +#--------------------------------------- + +#--------------------------------------- +# Total_sequences: 5 +# Total_hitcount: 5 +#--------------------------------------- |