Mercurial > repos > iuc > bio_hansel
diff bio_hansel.xml @ 1:4deefd708943 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
| author | iuc |
|---|---|
| date | Thu, 06 May 2021 18:31:35 +0000 |
| parents | e3698ac146d7 |
| children | 1b88c1cf803d |
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--- a/bio_hansel.xml Tue Oct 03 10:39:11 2017 -0400 +++ b/bio_hansel.xml Thu May 06 18:31:35 2021 +0000 @@ -1,47 +1,51 @@ -<tool id="bio_hansel" name="Salmonella Subtyping" version="0.1.0"> - <requirements> - <requirement type="package" version="0.1.0">bio_hansel</requirement> - <requirement type="package" version="17.2.0">attrs</requirement> - </requirements> +<tool id="bio_hansel" name="Salmonella Subtyping" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - ## Preparing file input. #if $data_type.type == "paired": - - ln -s '$data_type.fastq_input1' fast_q_paired_1.fastq && - ln -s '$data_type.fastq_input2' fast_q_paired_2.fastq && - + #if $data_type.fastq_input1.ext.endswith('.gz'): + gunzip -c '$data_type.fastq_input1' > fast_q_paired_1.fastq && + gunzip -c '$data_type.fastq_input2' > fast_q_paired_2.fastq && + #else: + ln -s '$data_type.fastq_input1' fast_q_paired_1.fastq && + ln -s '$data_type.fastq_input2' fast_q_paired_2.fastq && + #end if #elif $data_type.type == "collection": - - ln -s '$data_type.fastq_input1.forward' fast_q_paired_1.fastq && - ln -s '$data_type.fastq_input1.reverse' fast_q_paired_2.fastq && - - #elif $data_type.type == "single": - - #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): - ln -s '$data_type.fastq_input1' fast_q_single.fastq && + #if $data_type.fastq_input1.forward.ext.endswith('.gz'): + gunzip -c '$data_type.fastq_input1.forward' > fast_q_paired_1.fastq && + gunzip -c '$data_type.fastq_input2.reverse' > fast_q_paired_2.fastq && + #else: + ln -s '$data_type.fastq_input1.forward' fast_q_paired_1.fastq && + ln -s '$data_type.fastq_input1.reverse' fast_q_paired_2.fastq && #end if - - #if $data_type.fastq_input1.is_of_type('fasta'): - ln -s '$data_type.fastq_input1' fast_a_single.fasta && - #end if - - #end if - - - ## Checking for custom scheme. - #if $type_of_scheme.scheme_type == "custom": - #if $type_of_scheme.scheme_input.is_of_type('fasta'): - ln -s '$type_of_scheme.scheme_input' custom_scheme.fasta && + #elif $data_type.type == "single": + #if $data_type.fastq_input1.ext.startswith("fastq"): + #if $data_type.fastq_input1.ext.endswith('.gz'): + gunzip -c '$data_type.fastq_input1' > fast_q_single.fastq && + #else: + ln -s '$data_type.fastq_input1' fast_q_single.fastq && + #end if + #elif $data_type.fastq_input1.ext.startswith('fasta'): + #if $data_type.fastq_input1.ext.endswith('.gz'): + gunzip -c '$data_type.fastq_input1' > fast_a_single.fasta && + #else: + ln -s '$data_type.fastq_input1' fast_a_single.fasta && + #end if #end if #end if - - ## Start the actual command here + #if $type_of_scheme.scheme_type == "custom": + #if $type_of_scheme.scheme_input.ext.startswith('fasta'): + #if $type_of_scheme.scheme_input.ext.endswith('.gz'): + gunzip -c '$type_of_scheme.scheme_input' > custom_scheme.fasta && + #else: + ln -s '$type_of_scheme.scheme_input' custom_scheme.fasta && + #end if + #end if + #end if hansel - - - ## Select the scheme -s - #if $type_of_scheme.scheme_type == "heidelberg": heidelberg #elif $type_of_scheme.scheme_type == "enteritidis": @@ -49,36 +53,21 @@ #elif $type_of_scheme.scheme_type == "custom": custom_scheme.fasta #end if - - #if $kmer_min --min-kmer-freq $kmer_min #end if - #if $kmer_max --max-kmer-freq $kmer_max #end if - - ## Adding more parameters to the command. - -vvv -t "\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab - - - ## Entering the file inputs. + -vvv -t \${GALAXY_SLOTS:-1} -o 'results.tab' -O 'match_results.tab' #if $data_type.type == "single": - - #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'): + #if $data_type.fastq_input1.ext.startswith('fastq'): fast_q_single.fastq - #end if - - #if $data_type.fastq_input1.is_of_type('fasta'): + #elif $data_type.fastq_input1.ext.startswith('fasta'): fast_a_single.fasta #end if - #else - - ##use -p to declare using two files. -p fast_q_paired_1.fastq fast_q_paired_2.fastq - #end if ]]></command> <inputs> @@ -89,14 +78,14 @@ <option value="collection">Collection Paired-end Data</option> </param> <when value="single"> - <param name="fastq_input1" type="data" format="fastqsanger, fastq, fasta" label="Single end read file(s)"/> + <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz" label="Single end read file(s)"/> </when> <when value="paired"> - <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/> - <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/> + <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/> + <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/> </when> <when value="collection"> - <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" /> + <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" /> </when> </conditional> <conditional name="type_of_scheme"> @@ -108,49 +97,31 @@ <when value="heidelberg"/> <when value="enteritidis"/> <when value="custom"> - <param name="scheme_input" type="data" format="fasta" label="Scheme Input"/> + <param name="scheme_input" type="data" format="fasta,fasta.gz" label="Scheme Input"/> </when> </conditional> <param name="kmer_min" argument="--min-kmer-freq" optional="True" type="integer" min="0" label="Min k-mer freq/coverage" help="default = 10"/> <param name="kmer_max" argument="--max-kmer-freq" optional="True" type="integer" min="1" label="Max k-mer freq/coverage" help="default = 200"/> </inputs> <outputs> - <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/> - <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/> + <data format="tabular" name="results" from_work_dir="results.tab" label="${tool.name} on ${on_string}: results.tab"/> + <data format="tabular" name="match_results" from_work_dir="match_results.tab" label="${tool.name} on ${on_string}: match_results.tab"/> </outputs> <tests> <test> <param name="type" value="single"/> <param name="type_of_scheme" value="heidelberg"/> - <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/> - <output name="results.tab"> - <assert_contents> - <!-- Verifying that the columns are as expected. --> - <has_text_matching expression="sample\s+scheme\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_total\s+n_tiles_matching_positive\s+n_tiles_matching_positive_total\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_total\s+file_path"/> - <!-- Verifying that the output of running the test file is expected. This is done via REGEX because the name and path of the file outputted to results.tab changes each test. --> - <has_text_matching expression="(heidelberg)\s+(2.2.2.2.1.4)\s+(2;)\s+(2.2;)\s+(2.2.2;)\s+(2.2.2.2;)\s+(2.2.2.2.1;)\s+(2.2.2.2.1.4)\s+(1037658-2.2.2.2.1.4;)\s+(2154958-2.2.2.2.1.4;)\s+(3785187-2.2.2.2.1.4)\s+(True)\s+(202)\s+(202)\s+(17)\s+(17)\s+(3)\s+(3)"/> - </assert_contents> - </output> - <output name="match_results.tab"> - <assert_contents> - <!-- This is the last line in the file, this assertion is to make sure that we have the correct number of items. --> - <has_text_matching expression="negative4738855-1.1"/> - </assert_contents> - </output> + <param name="fastq_input1" ftype="fasta.gz" value="SRR1002850_SMALL.fasta.gz"/> + <output name="results" ftype="tabular" file="results1.tab" compare="contains"/> + <output name="match_results" ftype="tabular" file="match_results1.tab" compare="contains"/> </test> <test> <param name="type" value="paired"/> <param name="type_of_scheme" value="heidelberg"/> - <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/> - <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/> - <output name="results.tab"> - <assert_contents> - <!-- Verifying that the columns are as expected. --> - <has_text_matching expression="sample\s+scheme\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_total\s+n_tiles_matching_positive\s+n_tiles_matching_positive_total\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_total\s+file_path"/> - <!-- Verifying that the output of running the test file is expected. This is done via REGEX because the name and path of the file outputted to results.tab changes each test. --> - <has_text_matching expression="(heidelberg)\s+(2.2.1.1.1.1)\s+(2;)\s+(2.2;)\s+(2.2.1;)\s+(2.2.1.1;)\s+(2.2.1.1.1;)\s+(2.2.1.1.1.1)\s+(1983064-2.2.1.1.1.1;)\s+(4211912-2.2.1.1.1.1)\s+(True)\s+(202)\s+(202)\s+(20)\s+(20)\s+(2)\s+(2)"/> - </assert_contents> - </output> + <param name="fastq_input1" ftype="fastq.gz" value="SRR5646583_SMALL_1.fastq.gz"/> + <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq.gz"/> + <output name="results" ftype="tabular" file="results2.tab" compare="contains"/> + <output name="match_results" ftype="tabular" file="match_results2.tab" compare="contains"/> </test> </tests> <help><![CDATA[ @@ -264,4 +235,4 @@ } }</citation> </citations> -</tool> \ No newline at end of file +</tool>