Mercurial > repos > nilesh > rseqc
diff rseqc_macros.xml @ 63:27e16a30667a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
| author | iuc |
|---|---|
| date | Tue, 09 Apr 2024 11:24:55 +0000 |
| parents | 473382134e56 |
| children |
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--- a/rseqc_macros.xml Wed Feb 22 15:06:01 2023 +0000 +++ b/rseqc_macros.xml Tue Apr 09 11:24:55 2024 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">5.0.1</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@TOOL_VERSION@">5.0.3</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@GALAXY_VERSION@">20.01</token> <xml name="requirements"> <requirements> @@ -15,52 +15,41 @@ </xml> <xml name="stdio"> <stdio> - <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> - <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> + <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information"/> + <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information"/> </stdio> </xml> - <!-- Params --> <xml name="bam_param"> <param name="input" type="data" label="Input BAM file" format="bam" help="(--input-file)"/> </xml> - <xml name="bam_sam_param"> <param name="input" type="data" label="Input BAM/SAM file" format="bam,sam" help="(--input-file)"/> </xml> - <xml name="refgene_param"> <param argument="--refgene" type="data" format="bed12" label="Reference gene model" help="Reference gene model in BED fomat"/> </xml> - <xml name="mapq_param"> - <param argument="--mapq" type="integer" label="Minimum mapping quality" value="30" - help="Minimum mapping quality for an alignment to be considered as "uniquely mapped""/> + <param argument="--mapq" type="integer" label="Minimum mapping quality" value="30" help="Minimum mapping quality for an alignment to be considered as "uniquely mapped""/> </xml> - <xml name="readlength_param"> <param argument="--read-align-length" type="integer" value="" label="Alignment length" optional="false" help="Alignment length of read, usually set to the orignial read length"/> </xml> - <xml name="readnum_param"> <param argument="--read-num" type="integer" label="Number of aligned reads" value="1000000" help="Number of aligned reads with mismatches used to calculate the mismatch profile"/> </xml> - <xml name="sample_size_param"> <param argument="--sample-size" type="integer" label="Number of reads sampled" value="200000" min="1" help="Number of reads sampled from SAM/BAM file"/> </xml> - <xml name="min_intron_param"> - <param argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50" /> + <param argument="--min-intron" type="integer" value="50" label="Minimum intron length (bp)" help="Default: 50"/> </xml> - <xml name="layout_param"> <param name="layout" type="select" label="Sequencing layout" help="(--sequencing)"> <option value="SE" selected="true">Single-end</option> <option value="PE">Paired-end</option> </param> </xml> - <xml name="strand_type_param"> <conditional name="strand_type"> <param name="strand_specific" type="select" label="Strand-specific?"> @@ -69,21 +58,20 @@ <option value="single">Single-End RNA-seq</option> </param> <when value="pair"> - <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" help="(--strand)"> - <option value="sd" selected="true"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option> - <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option> + <param name="pair_type" type="select" display="radio" label="Pair-End Read Type (format: mapped --> parent)" help="(--strand)"> + <option value="sd" selected="true"> read1 (positive --> positive; negative --> negative), read2 (positive --> negative; negative --> positive)</option> + <option value="ds">read1 (positive --> negative; negative --> positive), read2 (positive --> positive; negative --> negative)</option> </param> </when> <when value="single"> - <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" help="(--strand)"> - <option value="s" selected="true">positive --> positive; negative --> negative</option> - <option value="d">positive --> negative; negative --> positive</option> + <param name="single_type" type="select" display="radio" label="Single-End Read Type (format: mapped --> parent)" help="(--strand)"> + <option value="s" selected="true">positive --> positive; negative --> negative</option> + <option value="d">positive --> negative; negative --> positive</option> </param> </when> - <when value="none"></when> + <when value="none"/> </conditional> </xml> - <xml name="multihits_param"> <conditional name="multihits_type"> <param name="multihits_type_selector" type="select" label="Reads with multiple hits" help="(--skip-multi-hits)"> @@ -91,34 +79,26 @@ <option value="skip_multihits">Skip Multiple Hit Reads/Only Use Uniquely Mapped Reads</option> </param> <when value="skip_multihits"> - <expand macro="mapq_param" /> + <expand macro="mapq_param"/> </when> - <when value="use_multihits" /> + <when value="use_multihits"/> </conditional> </xml> - <xml name="rscript_output_param"> - <param name="rscript_output" type="boolean" value="false" label="Output R-Script" - help="Output the R-Script used to generate the plots" /> + <param name="rscript_output" type="boolean" value="false" label="Output R-Script" help="Output the R-Script used to generate the plots"/> </xml> - - <!-- Output --> - <xml name="pdf_output_data" token_filename="output.pdf" token_label="${tool.name} on ${on_string}: PDF"> - <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="@LABEL@" /> + <data format="pdf" name="outputpdf" from_work_dir="@FILENAME@" label="@LABEL@"/> </xml> - <xml name="xls_output_data" token_filename="output.xls" token_label="${tool.name} on ${on_string}: XLS"> - <data format="tabular" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@" /> + <data format="tabular" name="outputxls" from_work_dir="@FILENAME@" label="@LABEL@"/> </xml> - <xml name="rscript_output_data" token_filename="output.r" token_label="${tool.name} on ${on_string}: Rscript"> <data format="txt" name="outputr" from_work_dir="@FILENAME@" label="@LABEL@"> <filter>rscript_output</filter> </data> </xml> - <!-- Command --> <token name="@MULTIHITS@"><![CDATA[ #if str($multihits_type.multihits_type_selector) == "skip_multihits" @@ -126,7 +106,6 @@ --mapq=${multihits_type.mapq} #end if ]]></token> - <token name="@BAM_SAM_INPUTS@"><![CDATA[ #set $extension = str($input.ext) ln -s -f '${input}' 'input.${extension}' && @@ -134,7 +113,6 @@ ln -s -f '${input.metadata.bam_index}' 'input.bam.bai' && #end if ]]></token> - <token name="@ABOUT@"> ----- @@ -158,7 +136,6 @@ </token> - <xml name="citations"> <citations> <citation type="doi">10.1093/bioinformatics/bts356</citation>