| Previous changeset 0:aaa868913641 (2022-09-22) Next changeset 2:f355085dd2aa (2024-01-11) |
|
Commit message:
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit afc3449a0b68d43fd1179543815dfe23b951e157 |
|
modified:
macro.xml polypolish.xml |
| b |
| diff -r aaa868913641 -r bd2a15dbcea1 macro.xml --- a/macro.xml Thu Sep 22 07:51:48 2022 +0000 +++ b/macro.xml Fri Oct 20 12:41:27 2023 +0000 |
| [ |
| @@ -1,7 +1,7 @@ <macros> <token name="@TOOL_VERSION@">0.5.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.05</token> <token name="@THREADS@">\${GALAXY_SLOTS:-7}</token> <xml name="version_command"> @@ -33,8 +33,8 @@ <option value="non_filter"> No filtering step</option> </param> <when value="filter"> - <param name="low" argument="--low" type="float" min="0" value="0.1" label="Low percentile threshold" help="Select the lower value to remove [default: 0.1]"/> - <param name="high" argument="--high" type="float" min="0" value="99.9" label="High percentile threshold" help="Select the lower value to remove [default: 99.9]"/> + <param argument="--low" type="float" min="0" value="0.1" label="Low percentile threshold" help="Select the lower value to remove [default: 0.1]"/> + <param argument="--high" type="float" min="0" value="99.9" label="High percentile threshold" help="Select the lower value to remove [default: 99.9]"/> </when> <when value="non_filter"> </when> |
| b |
| diff -r aaa868913641 -r bd2a15dbcea1 polypolish.xml --- a/polypolish.xml Thu Sep 22 07:51:48 2022 +0000 +++ b/polypolish.xml Fri Oct 20 12:41:27 2023 +0000 |
| [ |
| b'@@ -14,25 +14,31 @@\n For single SAM\n ======================================*#\n #if $input.sam_data_type.sam_selector == \'single\'\n- #if $input.sam_data_type.single_sam.ext == \'unsorted.bam\'\n+ #if $input.sam_data_type.single_sam.is_of_type("unsorted.bam")\n samtools view -h $input.sam_data_type.single_sam > input_sam &&\n #elif $input.sam_data_type.single_sam.ext == \'sam\'\n ln -s $input.sam_data_type.single_sam input_sam &&\n+ #else\n+ echo "${input.sam_data_type.single_sam} not a sam/bam file"\n #end if\n polypolish input_data input_sam > \'$polished_fasta\'\n #*======================================\n For paired SAM\n ======================================*#\n #elif $input.sam_data_type.sam_selector == \'paired\'\n- #if $input.sam_data_type.R1_sam.ext == \'unsorted.bam\'\n+ #if $input.sam_data_type.R1_sam.is_of_type("unsorted.bam")\n samtools view -h $input.sam_data_type.R1_sam > sample_R1.sam &&\n #elif $input.sam_data_type.R1_sam.ext == \'sam\'\n ln -s \'$input.sam_data_type.R1_sam\' sample_R1.sam &&\n+ #else\n+ echo "${input.sam_data_type.single_sam} not a sam/bam file"\n #end if\n- #if $input.sam_data_type.R2_sam.ext == \'unsorted.bam\'\n+ #if $input.sam_data_type.R2_sam.is_of_type("unsorted.bam")\n samtools view -h $input.sam_data_type.R2_sam > sample_R2.sam &&\n #elif $input.sam_data_type.R2_sam.ext == \'sam\'\n ln -s \'$input.sam_data_type.R2_sam\' sample_R2.sam &&\n+ #else\n+ echo "${input.sam_data_type.single_sam} not a sam/bam file"\n #end if\n #if $input.sam_data_type.insert_filter.filter_select == \'filter\'\n polypolish_insert_filter.py --low \'$input.sam_data_type.insert_filter.low\'\n@@ -51,10 +57,12 @@\n #elif $input.sam_data_type.sam_selector == \'multiple_single\'\n mkdir single_collection &&\n #for $value, $single_sam in enumerate($input.sam_data_type.single_collection):\n- #if $single_sam.ext == \'unsorted.bam\'\n+ #if $single_sam.is_of_type("unsorted.bam")\n samtools view -h $single_sam > \'single_collection/$(single_sam.element_identifier).sam\' &&\n #elif $single_sam.ext == \'sam\'\n ln -s $single_sam \'single_collection/$(single_sam.element_identifier).$(single_sam.ext)\' &&\n+ #else\n+ echo "${single_sam} is not a sam/bam file"\n #end if\n #end for\n polypolish input_data single_collection/*.sam > \'$polished_fasta\'\n@@ -64,12 +72,12 @@\n #elif $input.sam_data_type.sam_selector == "multiple_paired"\n mkdir paired_collection &&\n #for $value, $paired_sam in enumerate($input.sam_data_type.paired_collection):\n- #if $paired_sam.forward.ext == \'unsorted.bam\'\n+ #if $paired_sam.forward.is_of_type("unsorted.bam")\n samtools view -h $paired_sam.forward > \'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam\' &&\n #else\n ln -s \'$paired_sam.forward\' \'paired_collection/forward_input$(value)$(paired_sam.forward.element_identifier).sam\' &&\n #end if\n- #if $paired_sam.reverse.ext == \'unsorted.bam\'\n+ #if $paired_sam.reverse.is_of_type("unsorted.bam")\n samtools view -h $paired_sam.reverse > \'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam\' &&\n #else\n ln -s \'$paired_sam.reverse\' \'paired_collection/reverse_input$(value)$(paired_sam.reverse.element_identifier).sam\' &&\n@@ -135,16 +143,16 @@\n </co'..b'rue" falsevalue="false" label="Keep per base information file"/>\n </section>\n </inputs>\n <outputs>\n@@ -343,9 +351,9 @@\n <param name="sam_selector" value="multiple_single"/>\n <param name="single_collection">\n <collection type="list">\n- <element name="R1_sam" value="aligned_test_file/alignement_R1.bam" ftype="unsorted.bam"/>\n- <element name="R1_bis_sam" value="aligned_test_file/alignement_R1_bis.bam" ftype="unsorted.bam"/>\n- <element name="R1_ter_sam" value="aligned_test_file/alignement_R1_ter.bam" ftype="unsorted.bam"/>\n+ <element name="R1_sam" value="aligned_test_file/alignement_R1.sam" ftype="sam"/>\n+ <element name="R1_bis_sam" value="aligned_test_file/alignement_R1_bis.sam" ftype="sam"/>\n+ <element name="R1_ter_sam" value="aligned_test_file/alignement_R1_ter.sam" ftype="sam"/>\n </collection>\n </param>\n </conditional>\n@@ -392,6 +400,34 @@\n </section>\n <output name="polished_fasta" value="polished.fasta"/>\n </test>\n+ <!-- Test_12 Test with bam files -->\n+ <test expect_num_outputs="1">\n+ <section name="input">\n+ <param name="fasta_file" value="contigs.fa"/>\n+ <conditional name="sam_data_type">\n+ <param name="sam_selector" value="single"/>\n+ <param name="single_sam" value="aligned_test_file/alignement_R1.bam"/>\n+ </conditional>\n+ </section>\n+ <output name="polished_fasta" value="polished.fasta"/>\n+ </test>\n+ <!-- Test_13 paired bam -->\n+ <test expect_num_outputs="2">\n+ <section name="input">\n+ <param name="fasta_file" value="contigs.fa"/>\n+ <conditional name="sam_data_type">\n+ <param name="sam_selector" value="paired"/>\n+ <param name="R1_sam" value="aligned_test_file/alignement_R1.bam"/>\n+ <param name="R2_sam" value="aligned_test_file/alignement_R2.bam"/>\n+ </conditional>\n+ </section>\n+ <section name="options">\n+ <param name="debug" value="true"/>\n+ <param name="keep_logfile" value="false"/>\n+ </section>\n+ <output name="polished_fasta" value="polished.fasta"/>\n+ <output name="debug_file" value="debug_file_test_2.tsv"/>\n+ </test>\n </tests>\n <help><![CDATA[\n **What it does**\n@@ -401,10 +437,12 @@\n \n **Polypolish pipeline steps**\n 1. [Optional] Filter aligned reads\n- - Exclude some alignments based on their insert size\n- - This should reduce the number of excessive alignments, particularly near the edges of repeat sequences, improving Polypolish\'s ability to fix errors in those regions.\n+ Exclude some alignments based on their insert size\n+ This should reduce the number of excessive alignments,\n+ particularly near the edges of repeat sequences, improving Polypolish\'s ability to fix errors in those regions.\n 2. Clean assembly with filtered reads\n \n+\n **Inputs**\n Polypolish need SAM/BAM input format obtain from aligner with option to keep all possible location\n Polypolish take on or more assembly as input fasta.\n@@ -414,9 +452,7 @@\n For example using bwa mem to align raw data before use, you need :\n 1. To align each read data independantly (also for paired data)\n 2. Set the option "Output all alignments for single-ends or unpaired paired-ends" in Select analysis mode>Set input/output options\n- - This allow multiple ailgnemnt output need to use polypolish\n-\n- \n+ This allow multiple ailgnemnt output need to use polypolish\n ]]></help>\n <expand macro="citations"/>\n </tool>\n' |