Mercurial > repos > iuc > semibin_generate_sequence_features
diff generate_sequence_features.xml @ 5:8ba0c2edf3f3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit ee5d87e278238478c8ecab4a2f73723323f179a7
| author | iuc |
|---|---|
| date | Sun, 10 Aug 2025 11:39:49 +0000 |
| parents | 0608cf7dc528 |
| children |
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--- a/generate_sequence_features.xml Fri Aug 01 21:26:47 2025 +0000 +++ b/generate_sequence_features.xml Sun Aug 10 11:39:49 2025 +0000 @@ -10,18 +10,29 @@ <expand macro="version"/> <command detect_errors="exit_code"><![CDATA[ #import re -@BAM_FILES@ +#if $input_type_select.input_type == "bam": + @BAM_FILES@ +#else: + #for $e in $input_type_select.mode.abundance: + #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) + ln -s '$e' '${identifier}.txt' && + #end for +#end if @FASTA_FILES@ SemiBin2 -#if $mode.select == 'single' or $mode.select == 'co' +#if $input_type_select.mode.select == 'single' or $input_type_select.mode.select == 'co' generate_sequence_features_single #else generate_sequence_features_multi --separator '$separator' #end if --input-fasta 'contigs.fasta' +#if $input_type_select.input_type == "bam" --input-bam *.bam +#else: + -a *.txt +#end if --output 'output' --threads \${GALAXY_SLOTS:-1} @MIN_LEN@ @@ -30,7 +41,18 @@ #end if ]]></command> <inputs> - <expand macro="mode_fasta_bam"/> + <conditional name="input_type_select"> + <param name="input_type" type="select" label="Use BAM or strobealign abundance information?"> + <option value="bam">BAM file</option> + <option value="txt">strobealign-aemb files</option> + </param> + <when value="bam"> + <expand macro="mode_fasta_bam"/> + </when> + <when value="txt"> + <expand macro="mode_fasta_strobealign"/> + </when> + </conditional> <expand macro="min_len"/> <expand macro="ml-threshold"/> <param name="extra_output" type="select" multiple="true" label="Extra outputs" help="In addition to the training data"> @@ -45,10 +67,13 @@ </outputs> <tests> <test expect_num_outputs="4"> - <conditional name="mode"> - <param name="select" value="single"/> - <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> - <param name="input_bam" ftype="bam" value="input_single.bam"/> + <conditional name="input_type_select"> + <param name="input_type" value="bam"/> + <conditional name="mode"> + <param name="select" value="single"/> + <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> + <param name="input_bam" ftype="bam" value="input_single.bam"/> + </conditional> </conditional> <conditional name="min_len"> <param name="method" value="automatic"/> @@ -83,10 +108,13 @@ </output> </test> <test expect_num_outputs="4"> - <conditional name="mode"> - <param name="select" value="co"/> - <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> - <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/> + <conditional name="input_type_select"> + <param name="input_type" value="bam"/> + <conditional name="mode"> + <param name="select" value="co"/> + <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> + <param name="input_bam" ftype="bam" value="input_coassembly_sorted1.bam,input_coassembly_sorted2.bam,input_coassembly_sorted3.bam,input_coassembly_sorted4.bam,input_coassembly_sorted5.bam"/> + </conditional> </conditional> <conditional name="min_len"> <param name="method" value="automatic"/> @@ -138,13 +166,16 @@ </output_collection> </test> <test expect_num_outputs="7"> - <conditional name="mode"> - <param name="select" value="multi"/> - <conditional name="multi_fasta"> - <param name="select" value="concatenated"/> - <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/> + <conditional name="input_type_select"> + <param name="input_type" value="bam"/> + <conditional name="mode"> + <param name="select" value="multi"/> + <conditional name="multi_fasta"> + <param name="select" value="concatenated"/> + <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/> + </conditional> + <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/> </conditional> - <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/> </conditional> <conditional name="min_len"> <param name="method" value="automatic"/> @@ -224,14 +255,87 @@ </element> </output_collection> </test> + + <test expect_num_outputs="5"> + <conditional name="input_type_select"> + <param name="input_type" value="txt"/> + <conditional name="mode"> + <param name="select" value="multi"/> + <conditional name="multi_fasta"> + <param name="select" value="concatenated"/> + <param name="input_fasta" ftype="fasta" value="input_multi.fasta.gz"/> + </conditional> + <param name="abundance" ftype="txt" value="strobealign_1.txt,strobealign_2.txt,strobealign_3.txt,strobealign_4.txt,strobealign_5.txt"/> + </conditional> + </conditional> + <conditional name="min_len"> + <param name="method" value="automatic"/> + </conditional> + <param name="ml_threshold" value="4000"/> + <param name="extra_output" value="coverage,contigs"/> + <output_collection name="multi_data" count="10"> + <element name="S1" ftype="csv"> + <assert_contents> + <has_n_lines n="21"/> + <has_text text="g1k_0"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="multi_data_split" count="10"> + <element name="S1" ftype="csv"> + <assert_contents> + <has_n_lines n="41"/> + <has_text text="g1k_0_1"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="multi_cov_sample" count="10"> + <element name="S1" ftype="csv"> + <assert_contents> + <has_n_lines n="21"/> + <has_text text="g1k_0"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="multi_split_cov_txt" count="10"> + <element name="S1" ftype="csv"> + <assert_contents> + <has_n_lines n="41"/> + <has_text text="g1k_5_1"/> + </assert_contents> + </element> + <element name="S9" ftype="csv"> + <assert_contents> + <has_n_lines n="41"/> + <has_text text="g1k_5_1"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="multi_contigs" count="10"> + <element name="S1" ftype="fasta"> + <assert_contents> + <has_text text=">g1k_0"/> + </assert_contents> + </element> + <element name="S9" ftype="fasta"> + <assert_contents> + <has_text text=">g1k_0"/> + </assert_contents> + </element> + </output_collection> + </test> + <test expect_num_outputs="2"> - <conditional name="mode"> - <param name="select" value="multi"/> - <conditional name="multi_fasta"> + <conditional name="input_type_select"> + <param name="input_type" value="bam"/> + <conditional name="mode"> <param name="select" value="multi"/> - <param name="input_fasta" ftype="fasta" value="S1.fasta,S2.fasta,S3.fasta,S4.fasta,S5.fasta,S6.fasta,S7.fasta,S8.fasta,S9.fasta,S10.fasta"/> + <conditional name="multi_fasta"> + <param name="select" value="multi"/> + <param name="input_fasta" ftype="fasta" value="S1.fasta,S2.fasta,S3.fasta,S4.fasta,S5.fasta,S6.fasta,S7.fasta,S8.fasta,S9.fasta,S10.fasta"/> + </conditional> + <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/> </conditional> - <param name="input_bam" ftype="bam" value="input_multi_sorted1.bam,input_multi_sorted2.bam,input_multi_sorted3.bam,input_multi_sorted4.bam,input_multi_sorted5.bam,input_multi_sorted6.bam,input_multi_sorted7.bam,input_multi_sorted8.bam,input_multi_sorted9.bam,input_multi_sorted10.bam"/> </conditional> <conditional name="min_len"> <param name="method" value="automatic"/>