| Previous changeset 68:a5a99218ef7a (2019-02-06) Next changeset 70:be25d16676f6 (2020-02-06) |
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Commit message:
planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit bd03f99240a3d174c1b22245fbdf45e15edb4a5e |
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modified:
sRNAPipe.xml |
| b |
| diff -r a5a99218ef7a -r fa794d2a5aaf sRNAPipe.xml --- a/sRNAPipe.xml Wed Feb 06 04:03:15 2019 -0500 +++ b/sRNAPipe.xml Tue Feb 12 04:11:07 2019 -0500 |
| [ |
| b'@@ -1,14 +1,14 @@\n <tool id="sRNAPipe" name="sRNAPipe" version="1.1">\n <description>In-depth study of small RNA</description>\n <macros>\n- <xml name="source" token_arg="Argument" token_build="Build argument">\n+ <xml name="source" token_arg="Argument" token_build="Build argument" token_ref="">\n <conditional name="source">\n- <param name="source" type="select" label="Will you select the database from your history or use a built-in index?">\n+ <param name="source" type="select" label="Will you select the reference database from your history or use a built-in index?">\n <option value="indexed">Use a built-in index</option>\n <option value="history">Use one from the history</option>\n </param>\n <when value="indexed">\n- <param name="indices" argument="@ARG@" type="select" label="Select a reference genome" help="Also use @BUILD@">\n+ <param name="indices" argument="@ARG@" type="select" label="Select @REF@">\n <options from_data_table="bwa_indexes">\n <filter type="sort_by" column="2" />\n <validator type="no_options" message="No indexes are available" />\n@@ -16,146 +16,186 @@\n </param>\n </when>\n <when value="history">\n- <param name="file" argument="@ARG@" type="data" format="fasta" label="Select a reference from history" />\n+ <param name="file" argument="@ARG@" type="data" format="fasta" label="Select @REF@ from history" help="We will also use @BUILD@"/>\n </when>\n </conditional>\n </xml>\n+ <xml name="conditional_source" token_arg="Argument" token_build="Build argument" token_ref="" token_name="">\n+ <conditional name="@NAME@">\n+ <param name="use_ref" type="select" label="Use @REF@?">\n+ <option value="true">Yes</option>\n+ <option value="false" selected="true">No</option>\n+ </param>\n+ <when value="true">\n+ <expand macro="source" arg="@ARG@" build="@BUILD@" ref="@REF@"/>\n+ </when>\n+ <when value="false"/>\n+ </conditional>\n+ </xml>\n </macros>\n <requirements>\n <requirement type="package" version="1.1">srnapipe</requirement>\n </requirements>\n <version_command>srnapipe | grep \'version\' | grep "version" | cut -d \' \' -f 3</version_command>\n <command detect_errors="aggressive"><![CDATA[\n- srnapipe\n-\n- --fastq \'${first_input}\'\n- --fastq_n \'${first_input.name}\'\n- #for $input_file in $input_files:\n- --fastq \'${input_file.additional_input}\'\n- --fastq_n \'${input_file.additional_input.name}\'\n+srnapipe\n+ #if str($inputs.custom) == \'true\'\n+ #for $x in $inputs.inputs\n+ --fastq \'$x.fastq\'\n+ --fastq_n \'$x.fastq_n\'\n #end for\n-\n- #if $genome.source.source == "history":\n- --ref \'${genome.source.file}\'\n- --build_index\n- #else:\n- --ref \'${genome.source.indices.fields.path}\'\n- #end if\n+ #else\n+ #for $x in $inputs.fastq\n+ --fastq \'$x\'\n+ --fastq_n \'$x.element_identifier\'\n+ #end for\n+ #end if\n+ --min $min\n+ --max $max\n \n- #if $tRNAs.source.source == "history":\n- --tRNAs \'${tRNAs.source.file}\'\n- --build_tRNAs\n- #elif $tRNAs.source.source == "none":\n- --tRNAs "None"\n- #else:\n- --tRNAs \'${tRNAs.source.indices.fields.path}\'\n- #end if\n+ #if $genome.source.source == "history"\n+ --ref \'$genome.source.file\'\n+ --build_index\n+ #else\n+ --ref \'$genome.source.indices.fields.path\'\n+ #end if\n+ --mis $genome.mis\n \n- #if $snRNAs.source.source == "history":\n- --snRNAs '..b' <param name="source" value="history" />\n <param name="file" value ="genome-small.fa" />\n </conditional>\n+ <param name="mis" value="0" />\n </section>\n <section name="transcripts">\n <conditional name="source">\n@@ -163,44 +203,54 @@\n <param name="file" value ="transcripts-file-small.fa" />\n </conditional>\n </section>\n- <section name="TE">\n+ <section name="te">\n <conditional name="source">\n <param name="source" value="history" />\n <param name="file" value ="TE-file-small.fa" />\n </conditional>\n+ <param name="misTE" value="3" />\n </section>\n- <section name="miRNAs">\n+ <section name="mirnas">\n <conditional name="source">\n <param name="source" value="history" />\n <param name="file" value ="mirbase-21-dme-hairpins-16jul2015.fa" />\n </conditional>\n </section>\n- <section name="snRNAs">\n- <conditional name="source">\n- <param name="source" value="history" />\n- <param name="file" value ="dmel-all-sn-snoRNA-r6.03.fasta" />\n+ <section name="snrnas">\n+ <conditional name="snrnas">\n+ <param name="use_ref" value="true"/>\n+ <conditional name="source">\n+ <param name="source" value="history" />\n+ <param name="file" value ="dmel-all-sn-snoRNA-r6.03.fasta" />\n+ </conditional>\n </conditional>\n </section>\n- <section name="rRNAs">\n- <conditional name="source">\n- <param name="source" value="history" />\n- <param name="file" value ="dmel-all-rRNA-r6.03.fasta" />\n+ <section name="rrnas">\n+ <conditional name="rrnas">\n+ <param name="use_ref" value="true"/>\n+ <conditional name="source">\n+ <param name="source" value="history" />\n+ <param name="file" value ="dmel-all-rRNA-r6.03.fasta" />\n+ </conditional>\n </conditional>\n </section>\n- <section name="tRNAs">\n- <conditional name="source">\n- <param name="source" value="history" />\n- <param name="file" value ="dmel-all-tRNA-r6.03.fasta" />\n+ <section name="trnas">\n+ <conditional name="trnas">\n+ <param name="use_ref" value="true"/>\n+ <conditional name="source">\n+ <param name="source" value="history" />\n+ <param name="file" value ="dmel-all-tRNA-r6.03.fasta" />\n+ </conditional>\n </conditional>\n </section>\n- <param name="min" value="18" />\n- <param name="max" value="29" />\n- <param name="si_min" value="21" />\n- <param name="si_max" value="21" />\n- <param name="pi_min" value="23" />\n- <param name="pi_max" value="29" />\n- <param name="mis" value="0" />\n- <param name="misTE" value="3" />\n+ <section name="sirna">\n+ <param name="si_min" value="21" />\n+ <param name="si_max" value="21" />\n+ </section>\n+ <section name="pirna">\n+ <param name="pi_min" value="23" />\n+ <param name="pi_max" value="29" />\n+ </section>\n <param name="PPPon" value="true" />\n <output name=\'html_out\' file="res.html" compare=\'diff\' lines_diff = \'10\'/>\n <output_collection name="output_fastqsanger" type="list">\n' |