Mercurial > repos > iuc > stacks_denovomap
diff stacks_denovomap.xml @ 3:bab631cc9f64 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
| author | iuc |
|---|---|
| date | Sat, 25 Jun 2016 17:28:47 -0400 |
| parents | 9d588fb2aee5 |
| children | 998dfec32bde |
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--- a/stacks_denovomap.xml Wed Jun 15 06:24:47 2016 -0400 +++ b/stacks_denovomap.xml Sat Jun 25 17:28:47 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.0"> +<tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.1"> <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description> <macros> <import>macros.xml</import> @@ -13,11 +13,11 @@ #for $input_parent in $options_usage.parent_sequences: #if $input_parent.ext == "fastqsanger": - #set $data_path = splitext($input_parent.name)[0] + #set $data_path = splitext($input_parent.element_identifier)[0] #set $data_path = re.sub(r'\.1$', '', $data_path) #set $data_path = $data_path + ".fq" #else: - #set $data_path = splitext($input_parent.name)[0] + #set $data_path = splitext($input_parent.element_identifier)[0] #set $data_path = re.sub(r'\.1$', '', $data_path) #set $data_path = $data_path + ".fa" #end if @@ -26,28 +26,29 @@ #end for #for $input_progeny in $options_usage.progeny_sequences: + #if $input_progeny: + #if $input_progeny.ext == "fastqsanger": + #set $data_path = splitext($input_progeny.element_identifier)[0] + #set $data_path = re.sub(r'\.1$', '', $data_path) + #set $data_path = $data_path + ".fq" + #else: + #set $data_path = splitext($input_progeny.element_identifier)[0] + #set $data_path = re.sub(r'\.1$', '', $data_path) + #set $data_path = $data_path + ".fa" + #end if - #if $input_progeny.ext == "fastqsanger": - #set $data_path = splitext($input_progeny.name)[0] - #set $data_path = re.sub(r'\.1$', '', $data_path) - #set $data_path = $data_path + ".fq" - #else: - #set $data_path = splitext($input_progeny.name)[0] - #set $data_path = re.sub(r'\.1$', '', $data_path) - #set $data_path = $data_path + ".fa" + ln -s "${input_progeny}" "${data_path}" && #end if - - ln -s "${input_progeny}" "${data_path}" && #end for #else: #for $input_indiv in $options_usage.individual_sample: #if $input_indiv.ext == "fastqsanger": - #set $data_path = splitext($input_indiv.name)[0] + #set $data_path = splitext($input_indiv.element_identifier)[0] #set $data_path = re.sub(r'\.1$', '', $data_path) #set $data_path = $data_path + ".fq" #else: - #set $data_path = splitext($input_indiv.name)[0] + #set $data_path = splitext($input_indiv.element_identifier)[0] #set $data_path = re.sub(r'\.1$', '', $data_path) #set $data_path = $data_path + ".fa" #end if @@ -67,11 +68,11 @@ #if str( $options_usage.rad_analysis_type ) == "genetic": #for $input_parent in $options_usage.parent_sequences: #if $input_parent.ext == "fastqsanger": - #set $data_path = splitext($input_parent.name)[0] + #set $data_path = splitext($input_parent.element_identifier)[0] #set $data_path = re.sub(r'\.1$', '', $data_path) #set $data_path = $data_path + ".fq" #else: - #set $data_path = splitext($input_parent.name)[0] + #set $data_path = splitext($input_parent.element_identifier)[0] #set $data_path = re.sub(r'\.1$', '', $data_path) #set $data_path = $data_path + ".fa" #end if @@ -82,17 +83,19 @@ -A $options_usage.cross_type #for $input_progeny in $options_usage.progeny_sequences: - #if $input_progeny.ext == "fastqsanger": - #set $data_path = splitext($input_progeny.name)[0] - #set $data_path = re.sub(r'\.1$', '', $data_path) - #set $data_path = $data_path + ".fq" - #else: - #set $data_path = splitext($input_progeny.name)[0] - #set $data_path = re.sub(r'\.1$', '', $data_path) - #set $data_path = $data_path + ".fa" + #if $input_progeny: + #if $input_progeny.ext == "fastqsanger": + #set $data_path = splitext($input_progeny.element_identifier)[0] + #set $data_path = re.sub(r'\.1$', '', $data_path) + #set $data_path = $data_path + ".fq" + #else: + #set $data_path = splitext($input_progeny.element_identifier)[0] + #set $data_path = re.sub(r'\.1$', '', $data_path) + #set $data_path = $data_path + ".fa" + #end if + + -r "${data_path}" #end if - - -r "${data_path}" #end for #if str($assembly_options.P): @@ -102,11 +105,11 @@ #for $i_indiv, $input_indiv in enumerate($options_usage.individual_sample): #if $input_indiv.ext == "fastqsanger": - #set $data_path = splitext($input_indiv.name)[0] + #set $data_path = splitext($input_indiv.element_identifier)[0] #set $data_path = re.sub(r'\.1$', '', $data_path) #set $data_path = $data_path + ".fq" #else: - #set $data_path = splitext($input_indiv.name)[0] + #set $data_path = splitext($input_indiv.element_identifier)[0] #set $data_path = re.sub(r'\.1$', '', $data_path) #set $data_path = $data_path + ".fa" #end if @@ -156,16 +159,16 @@ <option value="population">Population</option> </param> <when value="genetic"> - <param name="parent_sequences" argument="-p" format="fastqsanger,fasta" type="data" multiple="true" label="Files containing parent sequences" help="Files containing parent sequences from a mapping cross" /> + <param name="parent_sequences" argument="-p" format="fastqsanger,fasta" type="data" multiple="true" label="Files containing parent sequences" help="Files containing parent sequences from a mapping cross (only R1 reads). Dataset names will be used as sample name (no space allowed)." /> - <param name="progeny_sequences" argument="-r" format="fastqsanger,fasta" type="data" multiple="true" optional="true" label="Files containing progeny sequences" help="files containing progeny sequences from a mapping cross" /> + <param name="progeny_sequences" argument="-r" format="fastqsanger,fasta" type="data" multiple="true" optional="true" label="Files containing progeny sequences" help="files containing progeny sequences from a mapping cross (only R1 reads). Dataset names will be used as sample name (no space allowed)." /> <param name="cross_type" argument="-A" type="select" label="Cross type"> <expand macro="cross_types"/> </param> </when> <when value="population"> - <param name="individual_sample" argument="-s" format="fastqsanger,fasta" type="data" multiple="true" label="Files containing an individual sample from a population" help="files containing an individual sample from a population" /> + <param name="individual_sample" argument="-s" format="fastqsanger,fasta" type="data" multiple="true" label="Files containing an individual sample from a population" help="files containing an individual sample from a population (only R1 reads). Dataset names will be used as sample name (no space allowed)." /> <param name="popmap" argument="-O" type="data" format="tabular,txt" label="Specify a population map" /> </when> </conditional> @@ -198,25 +201,25 @@ <expand macro="populations_output_light"/> <collection name="tags" type="list" label="Assembled loci from ${on_string}"> - <discover_datasets pattern="(?P<name>.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> <collection name="snps" type="list" label="Model calls from each locus on ${on_string}"> - <discover_datasets pattern="(?P<name>.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus on ${on_string}"> - <discover_datasets pattern="(?P<name>.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> <collection name="matches" type="list" label="Matches to the catalog on ${on_string}"> - <discover_datasets pattern="(?P<name>.+\.matches)\.tsv" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> <collection name="all_output" type="list" label="Full output from denovo_map on ${on_string}"> - <discover_datasets pattern="(?P<name>.+\.(tags|snps|alleles|matches))\.tsv" ext="tabular" directory="stacks_outputs" /> - <discover_datasets pattern="(?P<name>.+\.(haplotypes|genotypes|markers|hapstats|sumstats|sumstats_summary))\.tsv" ext="tabular" directory="stacks_outputs" /> - <discover_datasets pattern="(?P<name>.+\.(genotypes))\.(loc|txt)" ext="txt" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.(tags|snps|alleles|matches))\.tsv$" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.(haplotypes|genotypes|markers|hapstats|sumstats|sumstats_summary))\.tsv$" ext="tabular" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.(genotypes))\.(loc|txt)$" ext="txt" directory="stacks_outputs" /> </collection> </outputs> @@ -224,6 +227,85 @@ <test> <param name="options_usage|rad_analysis_type" value="genetic"/> <param name="options_usage|parent_sequences" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> + <output name="output_log"> + <assert_contents> + <has_text text="denovo_map.pl completed" /> + </assert_contents> + </output> + + <!-- catalog --> + <output name="catalogtags"> + <assert_contents> + <has_text text="catalog generated on" /> + </assert_contents> + </output> + <output name="catalogsnps"> + <assert_contents> + <has_text text="catalog generated on" /> + </assert_contents> + </output> + <output name="catalogalleles"> + <assert_contents> + <has_text text="catalog generated on" /> + </assert_contents> + </output> + + <!-- genotypes --> + <output name="out_generic_haplo"> + <assert_contents> + <has_text text="Catalog ID" /> + </assert_contents> + </output> + <output name="out_sql_markers"> + <assert_contents> + <has_text text="Total Genotypes" /> + </assert_contents> + </output> + <output name="out_joinmap"> + <assert_contents> + <has_text text="batch_1.genotypes_" /> + </assert_contents> + </output> + <output name="out_sql_genotypes"> + <assert_contents> + <has_text text="SQL ID" /> + </assert_contents> + </output> + + <!-- samples --> + <output_collection name="tags"> + <element name="PopA_01.tags"> + <assert_contents> + <has_text text="generated on " /> + </assert_contents> + </element> + </output_collection> + <output_collection name="snps"> + <element name="PopA_01.snps"> + <assert_contents> + <has_text text="generated on " /> + </assert_contents> + </element> + </output_collection> + <output_collection name="alleles"> + <element name="PopA_01.alleles"> + <assert_contents> + <has_text text="generated on " /> + </assert_contents> + </element> + </output_collection> + <output_collection name="matches"> + <element name="PopA_01.matches"> + <assert_contents> + <has_text text="generated on " /> + </assert_contents> + </element> + </output_collection> + </test> + + <test> + <param name="options_usage|rad_analysis_type" value="genetic"/> + <param name="options_usage|parent_sequences" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> <param name="options_usage|progeny_sequences" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" /> <output name="output_log"> <assert_contents> @@ -300,6 +382,7 @@ </element> </output_collection> </test> + <test> <param name="options_usage|rad_analysis_type" value="population"/> <param name="options_usage|individual_sample" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq,demultiplexed/PopA_03.1.fq,demultiplexed/PopA_04.1.fq,demultiplexed/PopB_01.1.fq,demultiplexed/PopB_02.1.fq,demultiplexed/PopB_03.1.fq,demultiplexed/PopB_04.1.fq" ftype="fastqsanger" />