# HG changeset patch # User ebi-gxa # Date 1599483994 0 # Node ID 2472523c0c50d2197999d81bc5be2f1ee3619f6c "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty" diff -r 000000000000 -r 2472523c0c50 scanpy-integrate-combat.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy-integrate-combat.xml Mon Sep 07 13:06:34 2020 +0000 @@ -0,0 +1,78 @@ + + + adjust expression for variables that might introduce batch effect + + scanpy_macros2.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 2472523c0c50 scanpy_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros.xml Mon Sep 07 13:06:34 2020 +0000 @@ -0,0 +1,109 @@ + + 1.3.2 + More information can be found at https://scanpy.readthedocs.io + +#if $do_plotting.plot + -P output.png + --projectio $do_plotting.projection + --components $do_plotting.components + #if $do_plotting.color_by + --color-by $do_plotting.color_by + #end if + #if $do_plotting.groups + --group $do_plotting.groups + #end if + #if $do_plotting.use_raw + --use-raw + #end if + #if $do_plotting.palette + --palette $do_plotting.palette + #end if + #if $do_plotting.edges + --edges + #end if + #if $do_plotting.arrows + --arrows + #end if + #if not $do_plotting.sort_order + --no-sort-order + #end if + #if $do_plotting.frameoff + --frameoff + #end if +#end if + + + + scanpy-scripts + + + + + ${export_mtx} + + + + + 10.1186/s13059-017-1382-0 + + @misc{githubscanpy-scripts, + author = {Ni Huang, EBI Gene Expression Team}, + year = {2018}, + title = {Scanpy-scripts: command line interface for Scanpy}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/scanpy-scripts}, + } + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + export_mtx + + + export_mtx + + + export_mtx + + + diff -r 000000000000 -r 2472523c0c50 scanpy_macros2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scanpy_macros2.xml Mon Sep 07 13:06:34 2020 +0000 @@ -0,0 +1,146 @@ + + 1.6.0 + More information can be found at https://scanpy.readthedocs.io + 18.01 + =1.4.2). + +1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files. + +1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute. + ]]> + + --input-format '${input_format}' input.h5 + + +#if str($output_format).startswith('anndata') + --show-obj stdout --output-format anndata output.h5 +#else + --show-obj stdout --output-format loom output.h5 +#end if + + +#if $fig_title + --title '${fig_title}' +#end if + --fig-size '${fig_size}' + --fig-dpi ${fig_dpi} + --fig-fontsize ${fig_fontsize} + ${fig_frame} + ./output.png + + ${export_mtx} + + + + scanpy-scripts + + + + + + + + 10.1186/s13059-017-1382-0 + + @misc{githubscanpy-scripts, + author = {Ni Huang, EBI Gene Expression Team}, + year = {2018}, + title = {Scanpy-scripts: command line interface for Scanpy}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/scanpy-scripts}, + } + 10.1101/2020.04.08.032698 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + output_format == 'anndata_h5ad' + + + output_format == 'anndata' + + + + + + output_format == 'anndata_h5ad' + + + output_format == 'anndata' + + + output_format == 'loom_legacy' + + + output_format == 'loom' + + + + + + + + + + + + + + + + + + export_mtx + + + export_mtx + + + export_mtx + + +