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Add bio.tools link to single-cell tools #6534

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Add bio.tools link to single-cell tools #6534

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0e107b8
Add hicexplorer bio tools ID
nomadscientist Nov 5, 2024
dc437f1
Update scHicAdjustMatrix.xml
nomadscientist Nov 5, 2024
729f79b
add biotools ref
nomadscientist Nov 5, 2024
5776dae
fix order
nomadscientist Nov 5, 2024
6f0d06e
add tool
nomadscientist Nov 5, 2024
9759cb4
add deg annotate bio.tools
nomadscientist Nov 5, 2024
53ebe50
add inferCNV
nomadscientist Nov 5, 2024
86f327b
add spapros
nomadscientist Nov 5, 2024
faaaa15
add velocyto
nomadscientist Nov 5, 2024
d5a8736
swap edam order
nomadscientist Nov 6, 2024
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3 changes: 3 additions & 0 deletions tools/crosscontamination_barcode_filter/crosscontamination_barcode_filter.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,9 @@
</sanitizer>
</macro>
</macros>
<xrefs>
<xref type="bio.tools">cross-contamination_barcode_filter</xref>
</xrefs>
<requirements>
<requirement type="package" version="3.1.1">r-ggplot2</requirement>
<requirement type="package" version="1.12.2">r-data.table </requirement>
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3 changes: 3 additions & 0 deletions tools/deg_annotate/deg_annotate.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
<tool id="deg_annotate" name="Annotate DESeq2/DEXSeq output tables" version="1.1.0">
<description>Append annotation from GTF to differential expression tool outputs</description>
<xrefs>
<xref type="bio.tools">deg_annotate</xref>
</xrefs>
<requirements>
<requirement type="package" version="2.27.0">bedtools</requirement>
<requirement type="package" version="0.6.4">bcbiogff</requirement>
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39 changes: 20 additions & 19 deletions tools/infercnv/infercnv.xml
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Expand Up @@ -3,6 +3,7 @@
<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements" />
<command detect_errors="exit_code"><![CDATA[
#if $annotation.gene_annotation == "gtf":
Expand All @@ -21,7 +22,7 @@
<configfile name="infercnv_script">
# InferCNV configuration file
# This file is used to specify the parameters for the InferCNV tool

# load library
library('infercnv')

Expand All @@ -47,10 +48,10 @@
#end if
delim="\t",
#if $max_cell:
max_cells_per_group = $max_cell, #maximun number of cells to use per group. Default=NULL, using all cells defined in the annotations_file.
max_cells_per_group = $max_cell, #maximun number of cells to use per group. Default=NULL, using all cells defined in the annotations_file.
#end if
#if $max_count:
min_max_counts_per_cell = c($min_count, $max_count), # minimum and maximum counts allowed per cell. Any cells outside this range will be removed from the counts matrix.
min_max_counts_per_cell = c($min_count, $max_count), # minimum and maximum counts allowed per cell. Any cells outside this range will be removed from the counts matrix.
#else
min_max_counts_per_cell = c($min_count, +Inf),
#end if
Expand All @@ -61,7 +62,7 @@
if (is.na(num_threads) || nchar(num_threads) == 0) {
num_threads = 1
}

# perform infercnv operations to reveal cnv signal
infercnv_obj = infercnv::run(
infercnv_obj,
Expand All @@ -81,10 +82,10 @@
## Clustering params
cluster_by_groups = $cluster_by_groups,
cluster_references = $cluster_references,
k_obs_groups = $k_obs_groups,
k_obs_groups = $k_obs_groups,
hclust_method = "$hclust_method",
max_centered_threshold = 3, # keep this as default
scale_data = $scale_data,
scale_data = $scale_data,

## HMM params
HMM= $HMM,
Expand Down Expand Up @@ -135,7 +136,7 @@
plot_steps = FALSE, # keep this as default
inspect_subclusters = TRUE, # keep this as default
resume_mode = TRUE, # keep this as default
png_res = $png_res,
png_res = $png_res,
plot_probabilities = TRUE, # keep this as default
save_rds = TRUE, # keep this as default
save_final_rds = TRUE, # keep this as default
Expand Down Expand Up @@ -163,9 +164,9 @@
#if str($median_filter) == "true":
infercnv_obj_medianfiltered = infercnv::apply_median_filtering(infercnv_obj)

infercnv::plot_cnv(infercnv_obj_medianfiltered,
infercnv::plot_cnv(infercnv_obj_medianfiltered,
out_dir='output',
output_filename='infercnv.median_filtered',
output_filename='infercnv.median_filtered',
obs_title = "Observations (Cells)", # keep this as default
ref_title = "References (Cells)", # keep this as default
cluster_by_groups = TRUE, # keep this as default
Expand All @@ -176,7 +177,7 @@
contig_cex = 1, # keep this as default
x.center = mean([email protected]), # keep this as default
x.range = "auto", # keep this as default
hclust_method = "$hclust_method",
hclust_method = "$hclust_method",
custom_color_pal = NULL, # keep this as default
color_safe_pal = FALSE, # keep this as default
png_res = $png_res,
Expand Down Expand Up @@ -588,19 +589,19 @@ InferCNV is compatible with both smart-seq2 and 10x single cell transcriptome da
The format might look like so:

======== ============= ============= ============= ============= ============= ================
, MGH54_P16_F12 MGH54_P12_C10 MGH54_P11_C11 MGH54_P15_D06 MGH54_P16_A03 ...
, MGH54_P16_F12 MGH54_P12_C10 MGH54_P11_C11 MGH54_P15_D06 MGH54_P16_A03 ...
-------- ------------- ------------- ------------- ------------- ------------- ----------------
A2M 0 0 0 0 0 ...
A2M 0 0 0 0 0 ...
-------- ------------- ------------- ------------- ------------- ------------- ----------------
A4GALT 0 0 0 0 0 ...
A4GALT 0 0 0 0 0 ...
-------- ------------- ------------- ------------- ------------- ------------- ----------------
AAAS 0 37 30 21 0 ...
AAAS 0 37 30 21 0 ...
-------- ------------- ------------- ------------- ------------- ------------- ----------------
AACS 0 0 0 0 2 ...
AACS 0 0 0 0 2 ...
-------- ------------- ------------- ------------- ------------- ------------- ----------------
AADAT 0 0 0 0 0 ...
AADAT 0 0 0 0 0 ...
-------- ------------- ------------- ------------- ------------- ------------- ----------------
... ... ... ... ... ... ...
... ... ... ... ... ... ...
======== ============= ============= ============= ============= ============= ================

The matrix can be provided as a tabular file, or ideally, as a 10x matrix market (sparse) format, as what the Seurat Read10x method expects (matrix.mtx, genes.tsv, barcodes.tsv).
Expand Down Expand Up @@ -658,7 +659,7 @@ UBE2J2 chr1 1189289 1209265

.. class:: infomark

Every gene in the counts matrix to be analyzed should have the corresponding gene name and location info provided in this gene ordering file.
Every gene in the counts matrix to be analyzed should have the corresponding gene name and location info provided in this gene ordering file.


.. class:: infomark
Expand Down Expand Up @@ -688,7 +689,7 @@ Note, only those genes that exist in both the counts matrix and the gene orderin

.. class:: infomark

**Note:**
**Note:**
By default, inferCNV operates at the level of whole samples, such as all cells defined as a certain cell type derived from a single patient. This is the fastest way to run inferCNV, but often not the optimal way, as a given tumor sample may have subpopulations with varied patterns of CNV.
By setting "analysis_mode" to "subclusters", inferCNV will attempt to partition cells into groups having consistent patterns of CNV. CNV prediction (via HMM) would then be performed at the level of the subclusters rather than whole samples.

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5 changes: 5 additions & 0 deletions tools/infercnv/macros.xml
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Expand Up @@ -2,6 +2,11 @@
<token name="@TOOL_VERSION@">1.20.0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@PROFILE@">21.09</token>
<xml name="xrefs">
<xrefs>
<xref type="bio.tools">infercnv</xref>
</xrefs>
</xml>
<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">bioconductor-infercnv</requirement>
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8 changes: 7 additions & 1 deletion tools/schicexplorer/macros.xml
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Expand Up @@ -3,6 +3,12 @@
<token name="@TOOL_VERSION@">4</token>
<token name="@PROFILE@">22.05</token>

<xml name="xrefs">
<xrefs>
<xref type="bio.tools">hicexplorer</xref>
</xrefs>
</xml>

<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">schicexplorer</requirement>
Expand Down Expand Up @@ -173,4 +179,4 @@
<option value="plasma_r">plasma reversed</option>
</param>
</xml>
</macros>
</macros>
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