Mercurial > repos > ebi-gxa > scanpy_scale_data

annotate scanpy-scale-data.xml @ 0:eae21a6c3128 draft

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author ebi-gxa
date Wed, 13 Mar 2019 11:50:13 -0400
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="scanpy_scale_data" name="Scanpy ScaleData" version="@TOOL_VERSION@+galaxy1">
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3 <description>to make expression variance the same for all genes</description>
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4 <macros>
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5 <import>scanpy_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '${input_obj_file}' input.h5 &&
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10 PYTHONIOENCODING=utf-8 scanpy-scale-data.py
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11 -i input.h5
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12 -f '${input_format}'
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13 -o output.h5
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14 -F '${output_format}'
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15 #if $scale_max
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16 -x '${scale_max}'
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17 #end if
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18 #if $var_to_regress
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19 -V '${var_to_regress}'
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20 #end if
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21 #if $do_log
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22 --do-log
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23 #end if
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24 #if $zero_center
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25 --zero-center
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26 #end if
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27 ]]></command>
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28
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29 <inputs>
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30 <expand macro="input_object_params"/>
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31 <expand macro="output_object_params"/>
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32 <param name="do_log" argument="--do-log" type="boolean" checked="true" label="Do log(x+1) transformation"/>
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33 <param name="zero_center" argument="--zero-center" type="boolean" checked="true" label="Zero center data before scaling"/>
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34 <param name="var_to_regress" argument="--var-to-regress" type="text" optional="true" label="Variable(s) to regress out">
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35 <option value="n_counts">n_counts</option>
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36 </param>
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37 <param name="scale_max" argument="--scale-max" type="float" optional="true" label="Truncate to this value after scaling"/>
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38 </inputs>
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39
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40 <outputs>
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41 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: Scaled data"/>
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42 </outputs>
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43
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44 <tests>
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45 <test>
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46 <param name="input_obj_file" value="find_variable_genes.h5"/>
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47 <param name="input_format" value="anndata"/>
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48 <param name="output_format" value="anndata"/>
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49 <param name="do_log" value="true"/>
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50 <param name="zero_center" value="true"/>
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51 <param name="scale_max" value="10"/>
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52 <output name="output_h5" file="scale_data.h5" ftype="h5" compare="sim_size"/>
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53 </test>
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54 </tests>
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55
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56 <help><![CDATA[
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57 .. class:: infomark
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58
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59 **What it does**
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60
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61 Scale data to unit variance and zero mean (`pp.scale`)
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62 Regress out unwanted sources of variation (`pp.regress_out`)
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63
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64 Regress out unwanted sources of variation, using simple linear regression. This is
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65 inspired by Seurat's `regressOut` function in R.
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66
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67 @HELP@
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68
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69 @VERSION_HISTORY@
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70 ]]></help>
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71 <expand macro="citations"/>
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72 </tool>