Main mutable

Author: natefoo

env/main/files/galaxy/var/integrated_tool_panel.xml

@@ -1009,6 +1009,10 @@
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.3+galaxy0" />
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.26.0+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0.0+galaxy0" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/fastq_quality_trimmer/1.1.5" />
@@ -1519,6 +1523,50 @@
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.15.1+galaxy2" />
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.6" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.8" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.6" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.5" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.6" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.3" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.5" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.5" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.6" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.4" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.4" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.2+galaxy3" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy3" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/samtools_depth/samtools_depth/1.21+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.21+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/samtools_fixmate/samtools_fixmate/1.21+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/samtools_markdup/samtools_markdup/1.21+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.21+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.21+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/samtools_ampliconclip/samtools_ampliconclip/1.21+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.21+galaxy3" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/samtools_coverage/samtools_coverage/1.20+galaxy3" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0" />
@@ -3351,6 +3399,34 @@
 
     <section id="interactive_tools" name="Interactive Tools" version="">
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/goeckslab/chatanalysis/interactive_tool_chat_analysis/0.1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/goeckslab/chatanalysis/interactive_tool_chat_analysis/0.2" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/goeckslab/chatanalysis/interactive_tool_chat_analysis/0.2.1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/goeckslab/chatanalysis/interactive_tool_chat_analysis/0.2.2" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/enis/interactive_tool_rstudio_bioconductor/interactive_tool_rstudio_bioconductor/4.5.0+3.21" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/goeckslab/chatanalysis/interactive_tool_chat_analysis/0.3.0" />
+
+        <tool id="interactive_tool_phyloseq" />
+
+        <tool id="interactive_tool_jupyter_notebook" />
+
+        <tool id="interactive_tool_panoply" />
+
+        <tool id="interactive_tool_phinch" />
+
+        <tool id="interactive_tool_pavian" />
+
+        <tool id="interactive_tool_qiskit_jupyter_notebook" />
+
+        <tool id="interactive_tool_blobtoolkit" />
+
+        <tool id="interactive_tool_rstudio" />
+
     </section>
 
     <section id="operate_on_genomic_intervals" name="Operate on Genomic Intervals" version="">
@@ -3855,6 +3931,10 @@
 
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.11+galaxy0" />
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/pairtools_dedup/pairtools_dedup/1.1.3+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/fastk_logex/fastk_logex/1.1.0+galaxy5" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/spades_metaviralspades/spades_metaviralspades/3.15.4+galaxy2" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0" />
@@ -4267,6 +4347,14 @@
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/icescreen/icescreen/1.3.3+galaxy0" />
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_egapx/ncbi_egapx/0.3.2+galaxy10" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_egapx/ncbi_egapx/0.3.2-alpha+galaxy7" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_egapx/ncbi_egapx/0.3.2-alpha+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_egapx/ncbi_egapx/0.3.2-alpha+galaxy6" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/richard-burhans/ncbi_egapx/ncbi_egapx/0.2-alpha+galaxy9" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/6.1.1+galaxy0" />
@@ -4775,6 +4863,10 @@
 
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.9+galaxy1" />
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.10+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.10+galaxy0" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/varscan_mpileup/varscan_mpileup/2.4.3.1" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/varscan_copynumber/varscan_copynumber/2.4.3.2" />
@@ -5311,6 +5403,8 @@
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11b+galaxy0" />
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0+galaxy1" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2" />
@@ -6545,6 +6639,34 @@
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/drep_dereplicate/drep_dereplicate/3.6.2+galaxy1" />
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_view/2.1.12+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/2.1.12+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/2.1.12+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/ufz/genomad_end_to_end/genomad_end_to_end/1.11.1+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/checkm_analyze/checkm_analyze/1.2.4+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/checkm_lineage_wf/checkm_lineage_wf/1.2.4+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/checkm_lineage_set/checkm_lineage_set/1.2.4+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/checkm_plot/checkm_plot/1.2.4+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/checkm_qa/checkm_qa/1.2.4+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/checkm_taxonomy_wf/checkm_taxonomy_wf/1.2.4+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/checkm_taxon_set/checkm_taxon_set/1.2.4+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/checkm_tetra/checkm_tetra/1.2.4+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/checkm_tree/checkm_tree/1.2.4+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/checkm_tree_qa/checkm_tree_qa/1.2.4+galaxy1" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_masking/2.8.3.0" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_alignment/2.8.3.0" />
@@ -10273,6 +10395,8 @@
 
         <tool id="toolshed.g2.bx.psu.edu/repos/goeckslab/pycaret_predict/pycaret_predict/3.3.2+1" />
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/goeckslab/tabular_learner/tabular_learner/0.1.0" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_pairwise_metrics/sklearn_pairwise_metrics/1.0.7.12" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_nn_classifier/sklearn_nn_classifier/1.0.7.12" />
@@ -11503,6 +11627,10 @@
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/seurat_reduce_dimension/seurat_reduce_dimension/5.0+galaxy0" />
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy10" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1" />
@@ -12653,6 +12781,10 @@
 
         <tool id="toolshed.g2.bx.psu.edu/repos/recetox/mfassignr_mfassign/mfassignr_mfassign/1.1.2+galaxy1" />
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/recetox/ramclustr/ramclustr/1.3.1+galaxy0" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/recetox/waveica/waveica/0.2.0+galaxy9" />
+
     </section>
 
     <section id="plots" name="Graph/Display Data" version="">
@@ -14439,6 +14571,12 @@
 
         <tool id="toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_plotting/scimap_plotting/2.1.0+galaxy2" />
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/2.1.0+galaxy3" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/2.1.0+galaxy3" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_plotting/scimap_plotting/2.1.0+galaxy3" />
+
     </section>
 
     <section id="rna_analysis" name="RNA Analysis" version="">

env/main/files/galaxy/var/sanitize_allowlist.txt

@@ -23,6 +23,8 @@ toolshed.g2.bx.psu.edu/repos/goeckslab/ludwig_hyperopt/ludwig_hyperopt
 toolshed.g2.bx.psu.edu/repos/goeckslab/ludwig_train/ludwig_train
 toolshed.g2.bx.psu.edu/repos/goeckslab/pycaret_compare
 toolshed.g2.bx.psu.edu/repos/goeckslab/pycaret_predict
+toolshed.g2.bx.psu.edu/repos/goeckslab/squidpy_spatial/squidpy_spatial
+toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial
 toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq
 toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp
 toolshed.g2.bx.psu.edu/repos/iuc/fastqe/fastqe

env/main/files/galaxy/var/shed_data_manager_conf.xml

@@ -890,4 +890,20 @@
             </output>
         </data_table>
     </data_manager>
+<data_manager id="genomad_build_database" guid="toolshed.g2.bx.psu.edu/repos/ufz/genomad_build_database/data_manager/genomad_build_database/0.0.1" shed_conf_file="/cvmfs/main.galaxyproject.org/config/shed_tool_conf.xml">
+        <tool file="toolshed.g2.bx.psu.edu/repos/ufz/genomad_build_database/34b729713d0c/genomad_build_database/data_manager/genomad_datamanager.xml" guid="toolshed.g2.bx.psu.edu/repos/ufz/genomad_build_database/genomad_build_database/1.11.1+galaxy0"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>genomad_build_database</repository_name><repository_owner>ufz</repository_owner><installed_changeset_revision>34b729713d0c</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/ufz/genomad_build_database/genomad_build_database/1.11.1+galaxy0</id><version>1.11.1+galaxy0</version></tool><data_table name="genomad">
+            <output>
+                <column name="value"/>
+                <column name="name"/>
+                <column name="path" output_ref="out_file">
+                    <move type="directory">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomad_databases/${value}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomad_databases/${value}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
 </data_managers>