comparison anndata_operations.xml @ 11:f0a29f4b9be9 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"

10:54f1212d26ac

<?xml version="1.0" encoding="utf-8"?>
<tool id="anndata_ops" name="AnnData Operations" version="0.0.3+galaxy0" profile="@PROFILE@">
  <description>modifies metadata and flags genes</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

import anndata
from numpy import all
import logging

adata = sc.read('input.h5')

gene_name = '${gene_symbols_field}'
qc_vars = list()

#for $i, $s in enumerate($modifications)

</configfiles>

  <inputs>
    <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in hdf5 AnnData format"/>
    <expand macro="output_object_params_no_loom"/>
    <repeat name="modifications" title="Change field names in AnnData observations" min="0">
      <param name="from_obs" type="text" label="Original name" help="Name in observations that you want to change">
        <sanitizer>
          <valid initial="string.printable"/>
        </sanitizer>

11:f0a29f4b9be9

<?xml version="1.0" encoding="utf-8"?>
<tool id="anndata_ops" name="AnnData Operations" version="0.0.3+galaxy1" profile="@PROFILE@">
  <description>modifies metadata and flags genes</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

import anndata
from numpy import all
import logging

adata = sc.read('input.h5')

#if $copy_adata_to_raw:
adata.raw = adata
#end if

gene_name = '${gene_symbols_field}'
qc_vars = list()

#for $i, $s in enumerate($modifications)

</configfiles>

  <inputs>
    <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in hdf5 AnnData format"/>
    <expand macro="output_object_params_no_loom"/>
    <param name="copy_adata_to_raw" type="boolean" label="Copy AnnData to .raw" help="If activated, it will do 'adata.raw = adata'" checked="false"/>
    <repeat name="modifications" title="Change field names in AnnData observations" min="0">
      <param name="from_obs" type="text" label="Original name" help="Name in observations that you want to change">
        <sanitizer>
          <valid initial="string.printable"/>
        </sanitizer>