| Previous changeset 0:384b9bcf2807 (2019-09-16) Next changeset 2:273d11a83e42 (2020-03-03) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 08ac0ad9182623944c4546f8ea8db6a1a537f7eb |
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modified:
monocle3-macros.xml monocle3-preprocess.xml |
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| diff -r 384b9bcf2807 -r 0869b0264af1 monocle3-macros.xml --- a/monocle3-macros.xml Mon Sep 16 09:50:29 2019 -0400 +++ b/monocle3-macros.xml Wed Jan 29 10:38:23 2020 -0500 |
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| @@ -1,9 +1,11 @@ <macros> - <token name="@TOOL_VERSION@">0.1.2</token> + <token name="@TOOL_VERSION@">0.1.3</token> <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/monocle3/ and https://github.com/ebi-gene-expression-group/monocle-scripts</token> <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +0.1.3+galaxy0: Updated to monocle3-cli 0.0.5 to fix bug with tsv inputs. + 0.1.2+galaxy0: Initial version based on monocle3-cli 0.0.3 and monocle3 0.1.2 ]]></token> <token name="@INPUT_OPTS@"> @@ -23,7 +25,7 @@ <xml name="requirements"> <requirements> - <requirement type="package" version="0.0.3">monocle3-cli</requirement> + <requirement type="package" version="0.0.5">monocle3-cli</requirement> <yield/> </requirements> </xml> @@ -57,7 +59,7 @@ </param> <param name="introspective" argument="--introspective" type="boolean" checked="true" label="Print introspective information of output object"/> </xml> - + <xml name="verbose_flag"> <param name="verbose" argument="--verbose" type="boolean" checked="false" label="Emit verbose output"/> </xml> |
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| diff -r 384b9bcf2807 -r 0869b0264af1 monocle3-preprocess.xml --- a/monocle3-preprocess.xml Mon Sep 16 09:50:29 2019 -0400 +++ b/monocle3-preprocess.xml Wed Jan 29 10:38:23 2020 -0500 |
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| @@ -16,7 +16,7 @@ --use-genes '${use_genes}' #end if #if $residual_model_formula_str - --residual-model-formula-str '~${residual_model_formula_str}' + --residual-model-formula-str '${residual_model_formula_str}' #end if #if $pseudo_count --pseudo-count '${pseudo_count}' @@ -44,7 +44,11 @@ <option value="size_only">Size factor correction only</option> </param> <param name="use_genes" argument="--use-genes" type="text" optional="true" label="Manually subset the gene pool to these genes for dimensionality reduction."/> - <param name="residual_model_formula_str" argument="--residual-model-formula-str" type="text" optional="true" label="A string model formula specifying effects to subtract from the data (excluding the leading ~)."/> + <param name="residual_model_formula_str" argument="--residual-model-formula-str" type="text" optional="true" label="A string model formula specifying effects to subtract from the data."> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> <param name="pseudo_count" argument="--pseudo-count" optional="true" type="float" value="1" label="Amount to increase expression values before dimensionality reduction."/> <param name="no_scaling" argument="--no-scaling" type="boolean" checked="false" label="When this option is NOT set, scale each gene before running trajectory reconstruction."/> <expand macro="verbose_flag"/> |