Mercurial > repos > mvdbeek > damidseq_core
changeset 3:e47f77820200 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit a76f114f428e08215ade1bd5cfebd86138243f75
author | mvdbeek |
---|---|
date | Sun, 26 Mar 2017 10:31:55 -0400 |
parents | 69e346fb52a0 |
children | b07936a3962d |
files | damidseq_core.xml |
diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
line wrap: on
line diff
--- a/damidseq_core.xml Thu Mar 23 12:11:32 2017 -0400 +++ b/damidseq_core.xml Sun Mar 26 10:31:55 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="damidseq_core" name="damidseq" version="0.1.2"> +<tool id="damidseq_core" name="damidseq" version="0.1.3"> <description>align, extend and normalize a DamID-seq experiment</description> <requirements> <requirement type="package" version="1.4">damidseq_pipeline</requirement> @@ -35,8 +35,8 @@ A2 Fusion</configfile> </configfiles> <inputs> + <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/> <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/> - <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="DAM fusion fastq"/> <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> <options from_data_table="bowtie2_indexes"> <filter type="sort_by" column="2"/> @@ -58,7 +58,7 @@ <param argument="--bins" type="integer" min="10" value="75" label="Width of bins to use for mapping reads"/> <param argument="--min_norm_value" type="float" value="-5.0" label="Minimum log2 value to limit normalisation search at"/> <param argument="--max_norm_value" type="float" value="5.0" label="Maximum log2 value to limit normalisation search at"/> - <param argument="--method_subtract" type="boolean" truevalue="--method_subtract" falsevalue="" label="Subtract DAM control values from DAM-fusion values instead of using the log2 ratio?"/> + <param argument="--method_subtract" type="boolean" truevalue="--method_subtract" falsevalue="" label="Subtract Dam control values from Dam-fusion values instead of using the log2 ratio?"/> <param argument="--norm_method" type="select" label="Select normalization method"> <option value="kde">kernel density estimation of log2 GATC fragment ratio (recommended)</option> <option value="rpm">readcounts per million reads (not recommended for most use cases)</option> @@ -70,7 +70,7 @@ <param argument="--qscore2max" type="float" min="0.0" value="0.9" max="1.0" label="max decile for normalising from fusion-protein array"/> </inputs> <outputs> - <data name="output_ratio" format="bed" from_work_dir="fusion.output" label="DAM-fusion vs Dam-only ratio"> + <data name="output_ratio" format="bed" from_work_dir="fusion.output" label="Dam-fusion vs Dam-only ratio"> <change_format> <when input="output_format" value="gff" format="gff" /> </change_format> @@ -83,7 +83,7 @@ </action> </actions> </data> - <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="DAM-only alignment"> + <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="Dam-only alignment"> <actions> <action type="metadata" name="dbkey"> <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> @@ -93,7 +93,7 @@ </action> </actions> </data> - <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="DAM-fusion alignment"> + <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="Dam-fusion alignment"> <actions> <action type="metadata" name="dbkey"> <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">