Mercurial > repos > ebi-gxa > sccaf_regress_out
annotate sccaf_regress_out.xml @ 1:5ef0610e9f50 draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
author | ebi-gxa |
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date | Mon, 25 Nov 2019 06:28:23 -0500 |
parents | 885db50f1bc1 |
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885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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1 <?xml version="1.0" encoding="utf-8"?> |
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5ef0610e9f50
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
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2 <tool id="sccaf_regress_out" name="SCCAF mulitple regress out" version="@TOOL_VERSION@+galaxy1"> |
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885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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3 <description>with multiple categorical keys on an AnnData object.</description> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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4 <macros> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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5 <import>sccaf_macros.xml</import> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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6 </macros> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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7 <expand macro="requirements"/> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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8 <command detect_errors="exit_code"><![CDATA[ |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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9 ln -s '${input_obj_file}' input.h5 && |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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10 sccaf-regress-out -i input.h5 -o output.h5 -k '${keys_to_regress}' |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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11 ]]></command> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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12 <inputs> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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13 <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 AnnData format"/> |
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5ef0610e9f50
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
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14 <expand macro="output_object_params"/> |
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885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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15 <param name="keys_to_regress" label="Keys to regress" help="Comma separated keys for regressing out; they need to exist in the observations part of the AnnData object." type="text"/> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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16 </inputs> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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17 <outputs> |
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5ef0610e9f50
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
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18 <expand macro="output_data_obj" description="regressed out on ${keys_to_regress}"/> |
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885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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19 </outputs> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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20 |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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21 <tests> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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22 <test> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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23 <param name="input_obj_file" value="find_cluster.h5"/> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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24 <param name="input_format" value="anndata"/> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
ebi-gxa
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25 <param name="color_by" value="louvain"/> |
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5ef0610e9f50
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 7034937deaaf56b2e6f585bb28234a86a5b5fa2e
ebi-gxa
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26 <output name="output_h5ad" file="output.h5" ftype="h5" compare="sim_size"/> |
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885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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27 </test> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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28 </tests> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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29 |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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30 <help><![CDATA[ |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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31 ============================= |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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32 Operations on AnnData objects |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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33 ============================= |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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34 |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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35 Performs the following operations: |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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36 |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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37 * Change observation fields, mostly for downstreaming processes convenience. Multiple fields can be changed as one. |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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38 * Flag genes that start with a certain text: useful for flagging mitochondrial, spikes or other groups of genes. |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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39 * For the flags created, calculates qc metrics (pct_<flag>_counts). |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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40 * Calculates `n_genes`, `n_counts` for cells and `n_cells`, `n_counts` for genes. |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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41 * For top <N> genes specified, calculate qc metrics (pct_counts_in_top_<N>_genes). |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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42 |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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43 This functionality will probably be added in the future to a larger package. |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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44 ]]></help> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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45 <!-- <expand macro="citations"/> --> |
885db50f1bc1
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf commit 39b0809db1e17c2a24930fe8fb8ceaf3ea454a7d
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46 </tool> |