Mercurial > repos > rnateam > paralyzer
diff paralyzer.xml @ 1:f880686a9194 draft default tip
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
| author | rnateam |
|---|---|
| date | Wed, 23 Oct 2019 19:07:22 -0400 |
| parents | 4dbe81be8b81 |
| children |
line wrap: on
line diff
--- a/paralyzer.xml Tue Dec 06 03:28:59 2016 -0500 +++ b/paralyzer.xml Wed Oct 23 19:07:22 2019 -0400 @@ -1,16 +1,13 @@ <tool id="paralyzer" name="PARalyzer" version="1.5"> - <description>A method to map interaction sites between RNA-binding proteins and their targets</description> - <requirements> <!-- conda dependency --> <requirement type="package" version="1.5">paralyzer</requirement> <requirement type="package" version="324">ucsc-fatotwobit</requirement> </requirements> + <command detect_errors="aggressive"><![CDATA[ - <command> -<![CDATA[ #if $refGenomeSource.genomeSource == "history": faToTwoBit '$refGenomeSource.ownFile' ownFile.2bit && @@ -24,6 +21,46 @@ ]]> </command> + <configfiles> + <configfile name="input_ini"> +## genome source +#if $refGenomeSource.genomeSource == "history": +GENOME_2BIT_FILE=ownFile.2bit +#else +GENOME_2BIT_FILE=$refGenomeSource.builtin.fields.path +#end if + +SAM_FILE=$input_sam$collapse + +#if $methods.choice == "ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL": +ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL=$methods.max_num +#else: +$methods.choice +#end if + +#if $conversion.selection == "custom": +CONVERSION=$conversion.character_from>$conversion.character_to +#end if + +## required parameters +#if $params.settingsType == "custom": +BANDWIDTH=$params.BANDWIDTH +MINIMUM_READ_COUNT_PER_GROUP=$params.min_read_group +MINIMUM_READ_COUNT_PER_CLUSTER=$params.min_read_cluster +MINIMUM_READ_COUNT_FOR_KDE=$params.min_read_kde +MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=$params.min_read_cluster_inc +MINIMUM_CLUSTER_SIZE=$params.min_cluster_size +MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=$params.min_conv_loc_cluster +MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=$params.min_conv_cluster +MINIMUM_READ_LENGTH=$params.min_read_len +MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=$params.max_num_conv_mis +#end if + +OUTPUT_DISTRIBUTIONS_FILE=out.distribution +OUTPUT_GROUPS_FILE=out.groups +OUTPUT_CLUSTERS_FILE=out.clusters + </configfile> + </configfiles> <inputs> <param name="input_sam" type="data" format="sam" label="Alignment" @@ -207,46 +244,6 @@ </when> <!-- full --> </conditional> </inputs> - <configfiles> - <configfile name="input_ini"> -## genome source -#if $refGenomeSource.genomeSource == "history": -GENOME_2BIT_FILE=ownFile.2bit -#else -GENOME_2BIT_FILE=$refGenomeSource.builtin.fields.path -#end if - -SAM_FILE=$input_sam$collapse - -#if $methods.choice == "ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL": -ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL=$methods.max_num -#else: -$methods.choice -#end if - -#if $conversion.selection == "custom": -CONVERSION=$conversion.character_from>$conversion.character_to -#end if - -## required parameters -#if $params.settingsType == "custom": -BANDWIDTH=$params.BANDWIDTH -MINIMUM_READ_COUNT_PER_GROUP=$params.min_read_group -MINIMUM_READ_COUNT_PER_CLUSTER=$params.min_read_cluster -MINIMUM_READ_COUNT_FOR_KDE=$params.min_read_kde -MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=$params.min_read_cluster_inc -MINIMUM_CLUSTER_SIZE=$params.min_cluster_size -MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=$params.min_conv_loc_cluster -MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=$params.min_conv_cluster -MINIMUM_READ_LENGTH=$params.min_read_len -MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=$params.max_num_conv_mis -#end if - -OUTPUT_DISTRIBUTIONS_FILE=out.distribution -OUTPUT_GROUPS_FILE=out.groups -OUTPUT_CLUSTERS_FILE=out.clusters - </configfile> - </configfiles> <outputs> <data name="distribution" format="txt" from_work_dir="out.distribution"